Tag: geneID

KEGG T07682: 118706260

Entry 118725205         ncRNA     T07682                                  Name (RefSeq) U1 spliceosomal RNA   KO K14276   U1 spliceosomal RNA Organism pkl  Pipistrellus kuhlii (Kuhl’s pipistrelle) Pathway pkl03040   Spliceosome Brite KEGG Orthology (KO) [BR:pkl00001] 09120 Genetic Information Processing  09121 Transcription   03040 Spliceosome    118725205 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03041 Spliceosome [BR:pkl03041]    118725205  09184 RNA family   03100 Non-coding RNAs [BR:pkl03100]    118725205Spliceosome [BR:pkl03041] Splicing related RNAs  118725205Non-coding RNAs [BR:pkl03100] Small non-coding…

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KEGG T01015: 4329963

Entry 4332822           CDS       T01015                                  Name (RefSeq) LOW QUALITY PROTEIN: nuclear cap-binding protein subunit 1-like   KO K12882   nuclear cap-binding protein subunit 1 Organism osa  Oryza sativa japonica (Japanese rice) (RefSeq) Pathway osa03013   Nucleocytoplasmic transport osa03015   mRNA surveillance pathway osa03040   Spliceosome Brite KEGG Orthology (KO) [BR:osa00001] 09120 Genetic Information Processing  09121 Transcription   03040 Spliceosome    4332822  09122 Translation   03013 Nucleocytoplasmic transport    4332822   03015 mRNA…

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KEGG T01710: 100306272

Entry 100782702         CDS       T01710                                  Symbol COX2 Name (RefSeq) cytochrome c oxidase subunit 2, mitochondrial   KO K02261   cytochrome c oxidase subunit 2 Organism gmx  Glycine max (soybean) Pathway gmx00190   Oxidative phosphorylation gmx01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:gmx00001] 09100 Metabolism  09102 Energy metabolism   00190 Oxidative phosphorylation    100782702 (COX2) 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03029 Mitochondrial biogenesis…

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No genes mapped in clusterprofiler gseGO

Hello! I’m having issues generating an adequate geneList for running gseGO in clusterProfiler, using keytype = “GO” Similar issues have been described here: No gene mapped gseGO code is: gse <- gseGO(geneList = gene_List, ont = “ALL”, #ont one of “BP”, “MF”, “CC” or “ALL” OrgDb = OrgDb, minGSSize =…

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Single-cell RNA-seq workflow

In this tutorial we walk through a typical single-cell RNA-seq analysis using Bioconductor packages. We will try to cover data from different protocols, but some of the EDA/QC steps will be focused on the 10X Genomics Chromium protocol. We start from the output of the Cell Ranger preprocessing software. This…

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how to merge human reference genome and GTF file with a custom sequence.

Hello Biostars, I am looking for some guidance on how to merge some files for my rna-bulk sequencing analysis. Let me start by describing the problem: I recieved an mRNA sequence of 4775 characters which I would like to merge with the human reference genome that I download from NCBI…

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Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome

Zachos, J., Pagani, H., Sloan, L., Thomas, E. & Billups, K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292, 686–693 (2001). Article  ADS  CAS  PubMed  Google Scholar  Favre, A. et al. The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan…

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Renaming fasta files with their headers

Renaming fasta files with their headers 1 Hi I have around 85 gene sequences in individual fasta files. I’d like to rename each file with their header name containing the gene name in [gene=]. For each header, I only want what is in-between the brackets. I’m trying to do this…

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Curated model organism gene functional annotations

Curated model organism gene functional annotations 0 Hi, I’m working with a model organism for the first time – C. elegans nematodes – and have created a list of differential expressed genes from some RNAseq data the lab had. One of the things I like to do is look for…

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Page not found at /GeneAnnotation/?id=Pzi006309&type=Pzijinensis

Page not found at /GeneAnnotation/?id=Pzi006309&type=Pzijinensis Using the URLconf defined in orchidbase5.urls, Django tried these URL patterns, in this order: ^admin/ ^rec_histone/$ [name=”main_algorithm”] Info_download/$ [name=”Info_download”] Sum_download/$ [name=”Sum_download”] example_download/$ [name=”example_download”] ^ ^$ [name=”home2020″] ^ ^geneinfo2022/ [name=”geneinfo2020″] ^ ^releaseSummary2022/ [name=”releaseSummary2020″] ^ ^orchidSpecies/ [name=”orchidSpecies”] ^ ^Contacts/ [name=”Contacts”] ^ ^Orchidbase4.0_user_guide/ [name=”Orchidbase4_user_guide”] ^ ^Orchidbase5.0_user_guide/ [name=”Orchidbase5_user_guide”] ^…

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Page not found at /GeneAnnotation/?id=Ash020296&type=Apostasia

Page not found at /GeneAnnotation/?id=Ash020296&type=Apostasia Using the URLconf defined in orchidbase6.urls, Django tried these URL patterns, in this order: ^admin/ ^home/ ^ ^tools/ [name=”tools”] ^ ^help/ [name=”Help”] ^ ^download/ [name=”download”] ^ ^Phalaenopsis_home/ [name=”Phalaenopsis_2020″] ^ ^Dendrobium_home/ [name=”Dendrobium_2020″] ^ ^Apostasia_home/ [name=”Apostasia_2020″] ^ ^Vpompona_home/ [name=”Vpompona_2020″] ^ ^Vshenzhenica_home/ [name=”Vshenzhenica_2020″] ^ ^Pguangdongensis_home/ [name=”Pguangdongensis_2020″] ^ ^Pzijinensis_home/…

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901-MG5 | Anti-XRCC1 (CHICKEN) Antibody Biotrend

Product Details Description: Anti-XRCC1 (CHICKEN) Antibody – 200-901-MG5 Synonyms: Chicken Anti-X-Ray Repair Cross Complementing 1 Antibody, X-Ray Repair Complementing Defective Repair In Chinese Hamster Cells 1, X-Ray Repair Cross-Complementing Protein 1, DNA Repair Protein XRCC1, SCAR26, RCC Host Species: Chicken Clonality: Polyclonal Format: IgY Target Details Gene Name: XRCC1  – View…

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KEGG T01005: 473325

Entry 473325            CDS       T01005                                  Symbol RNASE2 Name (RefSeq) non-secretory ribonuclease precursor   KO K01168   pancreatic ribonuclease [EC:4.6.1.18] Organism ptr  Pan troglodytes (chimpanzee) Brite KEGG Orthology (KO) [BR:ptr00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03019 Messenger RNA biogenesis [BR:ptr03019]    473325 (RNASE2)   04131 Membrane trafficking [BR:ptr04131]    473325 (RNASE2)Enzymes [BR:ptr01000] 4. Lyases  4.6  Phosphorus-oxygen lyases   4.6.1  Phosphorus-oxygen lyases (only sub-subclass identified to date)    4.6.1.18  pancreatic ribonuclease     473325 (RNASE2)Messenger…

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KEGG T01007: 415125

Entry 415125            CDS       T01007                                  Symbol FGFR2 Name (RefSeq) fibroblast growth factor receptor 2 precursor   KO K05093   fibroblast growth factor receptor 2 [EC:2.7.10.1] Organism cfa  Canis lupus familiaris (dog) Pathway cfa01521   EGFR tyrosine kinase inhibitor resistance cfa04010   MAPK signaling pathway cfa04014   Ras signaling pathway cfa04015   Rap1 signaling pathway cfa04020   Calcium signaling pathway cfa04144   Endocytosis…

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KEGG T02994: 18601618

Entry 18601618          CDS       T02994                                  Name (RefSeq) alpha-glucan phosphorylase 1   KO K00688   glycogen phosphorylase [EC:2.4.1.1] Organism tcc  Theobroma cacao (cacao) Pathway tcc00500   Starch and sucrose metabolism tcc01100   Metabolic pathways tcc01110   Biosynthesis of secondary metabolites Brite KEGG Orthology (KO) [BR:tcc00001] 09100 Metabolism  09101 Carbohydrate metabolism   00500 Starch and sucrose metabolism    18601618Enzymes [BR:tcc01000] 2. Transferases  2.4  Glycosyltransferases   2.4.1  Hexosyltransferases    2.4.1.1  glycogen phosphorylase     18601618 BRITE hierarchy SSDB OrthologParalogGene clusterGFIT…

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KEGG T02920: 102247935

Entry 102247935         CDS       T02920                                  Symbol TRMT44 Name (RefSeq) tRNA methyltransferase 44 homolog (S. cerevisiae)   KO K15447   tRNASer (uridine44-2′-O)-methyltransferase [EC:2.1.1.211] Organism myb  Myotis brandtii (Brandt’s bat) Brite KEGG Orthology (KO) [BR:myb00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03016 Transfer RNA biogenesis [BR:myb03016]    102247935 (TRMT44)Enzymes [BR:myb01000] 2. Transferases  2.1  Transferring one-carbon groups   2.1.1  Methyltransferases    2.1.1.211  tRNASer (uridine44-2′-O)-methyltransferase     102247935 (TRMT44)Transfer RNA biogenesis [BR:myb03016] Eukaryotic type  tRNA modification…

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KEGG T01001: 1474

Entry 1474              CDS       T01001                                  Symbol CST6, ECTD15 Name (RefSeq) cystatin E/M   KO K13902   cystatin-M Organism hsa  Homo sapiens (human) Disease H00651   Hypohidrotic ectodermal dysplasia Brite KEGG Orthology (KO) [BR:hsa00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01002 Peptidases and inhibitors [BR:hsa01002]    1474 (CST6)Peptidases and inhibitors [BR:hsa01002] Peptidase inhibitors  Family I25: cystatin family   1474 (CST6) BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif…

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KEGG T01001: 637

Entry 637               CDS       T01001                                  Symbol BID, FP497 Name (RefSeq) BH3 interacting domain death agonist   KO K04726   BH3 interacting domain death agonist Organism hsa  Homo sapiens (human) Pathway hsa01524   Platinum drug resistance hsa04071   Sphingolipid signaling pathway hsa04115   p53 signaling pathway hsa04210   Apoptosis hsa04215   Apoptosis – multiple species hsa04217   Necroptosis hsa04650   Natural killer cell mediated…

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KEGG T06063: 106511269

Entry 106522761         CDS       T06063                                  Symbol pak1 Name (RefSeq) serine/threonine-protein kinase PAK 1   KO K04409   p21-activated kinase 1 [EC:2.7.11.1] Organism alim  Austrofundulus limnaeus (annual killifish) Pathway alim04010   MAPK signaling pathway alim04012   ErbB signaling pathway alim04510   Focal adhesion alim04625   C-type lectin receptor signaling pathway alim04810   Regulation of actin cytoskeleton alim05132   Salmonella infection Brite KEGG Orthology…

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KEGG T01028: 706234

Entry 706234            CDS       T01028                                  Symbol TRAP1 Name (RefSeq) heat shock protein 75 kDa, mitochondrial   KO K09488   TNF receptor-associated protein 1 Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc05012   Parkinson disease mcc05022   Pathways of neurodegeneration – multiple diseases Brite KEGG Orthology (KO) [BR:mcc00001] 09160 Human Diseases  09164 Neurodegenerative disease   05012 Parkinson disease    706234 (TRAP1)   05022 Pathways of neurodegeneration –…

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Wheat Sequencing: The Pan-Genome and Opportunities for Accelerating Breeding

Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, Costa de Oliveira A, Cseke LJ, Dempewolf H, De Pace C, Edwards D, Gepts P, Greenland A, Hall AE, Henry R, Hori K, Howe GT, Hughes S, Humphreys M, Lightfoot D, Marshall A, Mayes S, Nguyen HT, Ogbonnaya…

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KEGG T03271: 103675060

Entry 103675060         CDS       T03271                                  Symbol APPL1 Name (RefSeq) DCC-interacting protein 13-alpha   KO K08733   DCC-interacting protein 13 alpha Organism umr  Ursus maritimus (polar bear) Pathway umr04211   Longevity regulating pathway umr05200   Pathways in cancer umr05210   Colorectal cancer Brite KEGG Orthology (KO) [BR:umr00001] 09150 Organismal Systems  09149 Aging   04211 Longevity regulating pathway    103675060 (APPL1) 09160 Human Diseases  09161 Cancer: overview   05200 Pathways in…

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KEGG T01001: 257194

Entry 257194            CDS       T01001                                  Symbol NEGR1, DMML2433, IGLON4, KILON, Ntra Name (RefSeq) neuronal growth regulator 1   KO K06775   neuronal growth regulator 1 Organism hsa  Homo sapiens (human) Pathway hsa04514   Cell adhesion molecules Brite KEGG Orthology (KO) [BR:hsa00001] 09130 Environmental Information Processing  09133 Signaling molecules and interaction   04514 Cell adhesion molecules    257194 (NEGR1) 09180 Brite Hierarchies  09183 Protein families: signaling…

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KEGG T08541: 104528229

Entry 104528229         CDS       T08541                                  Symbol SLC15A4 Name (RefSeq) solute carrier family 15 member 4   KO K14638   solute carrier family 15 (peptide/histidine transporter), member 3/4 Organism acar  Antrostomus carolinensis (chuck-will’s-widow) Brite KEGG Orthology (KO) [BR:acar00001] 09180 Brite Hierarchies  09183 Protein families: signaling and cellular processes   02000 Transporters [BR:acar02000]    104528229 (SLC15A4)Transporters [BR:acar02000] Solute carrier family (SLC)  SLC15: Proton oligopeptide cotransporter   104528229 (SLC15A4)…

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KEGG T01011: 100038077

Entry 100038077         CDS       T01011                                  Symbol nkx2-2 Name (RefSeq) homeobox protein Nkx-2.2 isoform X1   KO K08029   homeobox protein Nkx-2.2 Organism xtr  Xenopus tropicalis (tropical clawed frog) Brite KEGG Orthology (KO) [BR:xtr00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03000 Transcription factors [BR:xtr03000]    100038077 (nkx2-2)Transcription factors [BR:xtr03000] Eukaryotic type  Helix-turn-helix   Homeo domain ANTP: NKL    100038077 (nkx2-2) BRITE hierarchy SSDB OrthologParalogGene clusterGFIT…

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KEGG T09424: 118385109

Entry 118385109         CDS       T09424                                  Name (RefSeq) adenylosuccinate synthetase isozyme 2-like   KO K01939   adenylosuccinate synthase [EC:6.3.4.4] Organism oke  Oncorhynchus keta (chum salmon) Pathway oke00230   Purine metabolism oke00250   Alanine, aspartate and glutamate metabolism oke01100   Metabolic pathways oke01232   Nucleotide metabolism oke01240   Biosynthesis of cofactors Module oke_M00049   Adenine ribonucleotide biosynthesis, IMP => ADP,ATP Brite KEGG Orthology (KO)…

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KEGG T08782: 127423656

Entry 127423656         CDS       T08782                                  Name (RefSeq) heparan sulfate glucosamine 3-O-sulfotransferase 3B1-like   KO K07809   [heparan sulfate]-glucosamine 3-sulfotransferase 3 [EC:2.8.2.30] Organism masi  Myxocyprinus asiaticus (Chinese sucker) Pathway masi00534   Glycosaminoglycan biosynthesis – heparan sulfate / heparin Brite KEGG Orthology (KO) [BR:masi00001] 09100 Metabolism  09107 Glycan biosynthesis and metabolism   00534 Glycosaminoglycan biosynthesis – heparan sulfate / heparin    127423656 09180 Brite Hierarchies  09181 Protein…

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KEGG T01028: 701915

Entry 701915            CDS       T01028                                  Symbol KRT25 Name (RefSeq) keratin, type I cytoskeletal 25   KO K07604   type I keratin, acidic Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc04915   Estrogen signaling pathway mcc05150   Staphylococcus aureus infection Brite KEGG Orthology (KO) [BR:mcc00001] 09150 Organismal Systems  09152 Endocrine system   04915 Estrogen signaling pathway    701915 (KRT25) 09160 Human Diseases  09171 Infectious disease: bacterial   05150 Staphylococcus…

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KEGG T01028: 698365

Entry 698365            CDS       T01028                                  Symbol AMACR Name (RefSeq) alpha-methylacyl-CoA racemase   KO K01796   alpha-methylacyl-CoA racemase [EC:5.1.99.4] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc00120   Primary bile acid biosynthesis mcc01100   Metabolic pathways mcc04146   Peroxisome Module mcc_M00104   Bile acid biosynthesis, cholesterol => cholate/chenodeoxycholate Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism  09103 Lipid metabolism   00120 Primary bile acid biosynthesis    698365 (AMACR) 09140…

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KEGG T01028: 703937

Entry 703937            CDS       T01028                                  Symbol PTPRG Name (RefSeq) receptor-type tyrosine-protein phosphatase gamma isoform X2   KO K16667   receptor-type tyrosine-protein phosphatase gamma [EC:3.1.3.48] Organism mcc  Macaca mulatta (rhesus monkey) Brite KEGG Orthology (KO) [BR:mcc00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01009 Protein phosphatases and associated proteins [BR:mcc01009]    703937 (PTPRG)Enzymes [BR:mcc01000] 3. Hydrolases  3.1  Acting on ester bonds   3.1.3  Phosphoric-monoester hydrolases    3.1.3.48  protein-tyrosine-phosphatase     703937 (PTPRG)Protein phosphatases and…

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KEGG T07278: 119316072

Entry 119322531         CDS       T07278                                  Name (RefSeq) porphobilinogen deaminase, chloroplastic-like   KO K01749   hydroxymethylbilane synthase [EC:2.5.1.61] Organism tdc  Triticum dicoccoides (wild emmer wheat) Pathway tdc00860   Porphyrin metabolism tdc01100   Metabolic pathways tdc01110   Biosynthesis of secondary metabolites tdc01240   Biosynthesis of cofactors Module tdc_M00121   Heme biosynthesis, plants and bacteria, glutamate => heme Brite KEGG Orthology (KO) [BR:tdc00001] 09100 Metabolism  09108…

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Problem With Volcano Plot

Problem With Volcano Plot 0 Hi, I’m working with CMScaller and I’m performing the Volcano plot with the function: subVolcano. Usage subVolcano( deg, geneID = “rownames”, lfc = log2(2), padj = 0.05, ave = 0, topN = 10, cexText = 1, classCol = getOption(“subClassCol”), … ) But I have a…

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KEGG T01028: 704242

Entry 704242            CDS       T01028                                  Symbol CYP39A1 Name (RefSeq) 24-hydroxycholesterol 7-alpha-hydroxylase   KO K07439   24-hydroxycholesterol 7alpha-hydroxylase [EC:1.14.14.26] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc00120   Primary bile acid biosynthesis Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism  09103 Lipid metabolism   00120 Primary bile acid biosynthesis    704242 (CYP39A1) 09180 Brite Hierarchies  09181 Protein families: metabolism   00199 Cytochrome P450 [BR:mcc00199]    704242 (CYP39A1)Enzymes [BR:mcc01000] 1. Oxidoreductases  1.14  Acting on paired…

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KEGG T01028: 694719

Entry 694719            CDS       T01028                                  Symbol RPL23 Name (RefSeq) 60S ribosomal protein L23   KO K02894   large subunit ribosomal protein L23e Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc03010   Ribosome mcc05171   Coronavirus disease – COVID-19 Brite KEGG Orthology (KO) [BR:mcc00001] 09120 Genetic Information Processing  09122 Translation   03010 Ribosome    694719 (RPL23) 09160 Human Diseases  09172 Infectious disease: viral   05171 Coronavirus disease – COVID-19    694719…

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KEGG T08540: 104459063

Entry 104463828         CDS       T08540                                  Symbol ACOX3 Name (RefSeq) peroxisomal acyl-coenzyme A oxidase 3   KO K00232   acyl-CoA oxidase [EC:1.3.3.6] Organism pguu  Pterocles gutturalis (yellow-throated sandgrouse) Pathway pguu00071   Fatty acid degradation pguu00410   beta-Alanine metabolism pguu00592   alpha-Linolenic acid metabolism pguu00640   Propanoate metabolism pguu01040   Biosynthesis of unsaturated fatty acids pguu01100   Metabolic pathways pguu01200   Carbon metabolism pguu01212   Fatty…

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KEGG T01028: 704366

Entry 704366            CDS       T01028                                  Symbol ZDHHC15 Name (RefSeq) palmitoyltransferase ZDHHC15   KO K20028   palmitoyltransferase ZDHHC2/15/20 [EC:2.3.1.225] Organism mcc  Macaca mulatta (rhesus monkey) Brite KEGG Orthology (KO) [BR:mcc00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   04131 Membrane trafficking [BR:mcc04131]    704366 (ZDHHC15)Enzymes [BR:mcc01000] 2. Transferases  2.3  Acyltransferases   2.3.1  Transferring groups other than aminoacyl groups    2.3.1.225  protein S-acyltransferase     704366 (ZDHHC15)Membrane trafficking [BR:mcc04131] SNARE  SNARE associated proteins   Palmitoyltransferases    704366 (ZDHHC15) BRITE hierarchy…

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KEGG T01028: 695442

Entry 695442            CDS       T01028                                  Symbol RPLP1 Name (RefSeq) 60S acidic ribosomal protein P1   KO K02942   large subunit ribosomal protein LP1 Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc03010   Ribosome mcc05171   Coronavirus disease – COVID-19 Brite KEGG Orthology (KO) [BR:mcc00001] 09120 Genetic Information Processing  09122 Translation   03010 Ribosome    695442 (RPLP1) 09160 Human Diseases  09172 Infectious disease: viral   05171 Coronavirus disease –…

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KEGG T01028: 717682

Entry 717682            CDS       T01028                                  Symbol SEPTIN2 Name (RefSeq) septin-2 isoform X1   KO K16942   septin 2 Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc05100   Bacterial invasion of epithelial cells Brite KEGG Orthology (KO) [BR:mcc00001] 09160 Human Diseases  09171 Infectious disease: bacterial   05100 Bacterial invasion of epithelial cells    717682 (SEPTIN2) 09180 Brite Hierarchies  09182 Protein families: genetic information processing   04131 Membrane trafficking…

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KEGG T01028: 699325

Entry 699325            CDS       T01028                                  Symbol OSBP Name (RefSeq) oxysterol-binding protein 1   KO K20456   oxysterol-binding protein 1 Organism mcc  Macaca mulatta (rhesus monkey) Brite KEGG Orthology (KO) [BR:mcc00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   04131 Membrane trafficking [BR:mcc04131]    699325 (OSBP)Membrane trafficking [BR:mcc04131] Endoplasmic reticulum (ER) – Golgi transport  Others   Oxysterol-binding proteins    699325 (OSBP) BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif…

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KEGG T04128: 106346836

Entry 111199314         CDS       T04128                                  Name (RefSeq) GDP-L-fucose synthase 1 isoform X2   KO K02377   GDP-L-fucose synthase [EC:1.1.1.271] Organism bna  Brassica napus (rape) Pathway bna00051   Fructose and mannose metabolism bna00520   Amino sugar and nucleotide sugar metabolism bna01100   Metabolic pathways bna01250   Biosynthesis of nucleotide sugars Brite KEGG Orthology (KO) [BR:bna00001] 09100 Metabolism  09101 Carbohydrate metabolism   00051 Fructose and mannose…

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KEGG T01028: 706713

Entry 706713            CDS       T01028                                  Symbol HNMT Name (RefSeq) histamine N-methyltransferase   KO K00546   histamine N-methyltransferase [EC:2.1.1.8] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc00340   Histidine metabolism mcc01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism  09105 Amino acid metabolism   00340 Histidine metabolism    706713 (HNMT) 09180 Brite Hierarchies  09183 Protein families: signaling and cellular processes   04147 Exosome [BR:mcc04147]    706713 (HNMT)Enzymes [BR:mcc01000] 2. Transferases  2.1  Transferring…

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KEGG T01028: 694392

Entry 694392            CDS       T01028                                  Symbol WEE2 Name (RefSeq) wee1-like protein kinase 2   KO K06632   wee1-like protein kinase [EC:2.7.11.1] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc04110   Cell cycle mcc05170   Human immunodeficiency virus 1 infection Brite KEGG Orthology (KO) [BR:mcc00001] 09140 Cellular Processes  09143 Cell growth and death   04110 Cell cycle    694392 (WEE2) 09160 Human Diseases  09172 Infectious disease: viral   05170…

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KEGG T02386: 101070831

Entry 101070831         CDS       T02386                                  Symbol cldn3d Name (RefSeq) claudin-4   KO K06087   claudin Organism tru  Takifugu rubripes (torafugu) Pathway tru04514   Cell adhesion molecules tru04530   Tight junction Brite KEGG Orthology (KO) [BR:tru00001] 09130 Environmental Information Processing  09133 Signaling molecules and interaction   04514 Cell adhesion molecules    101070831 (cldn3d) 09140 Cellular Processes  09144 Cellular community – eukaryotes   04530 Tight junction    101070831 (cldn3d) 09180 Brite Hierarchies  09183 Protein…

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KEGG T01028: 693999

Entry 693999            CDS       T01028                                  Symbol POLI Name (RefSeq) DNA polymerase iota isoform X1   KO K03510   DNA polymerase iota [EC:2.7.7.7] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc03460   Fanconi anemia pathway Brite KEGG Orthology (KO) [BR:mcc00001] 09120 Genetic Information Processing  09124 Replication and repair   03460 Fanconi anemia pathway    693999 (POLI) 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03400 DNA…

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FPMs varying based on sample groups used

DESeq2: FPMs varying based on sample groups used 1 @2034d2f5 Last seen 10 hours ago Austria I recently analysed a transcriptomic dataset with 3 sample groups (4 samples each) and performed a pairwise comparison between the groups. I output the FPMs for the pairwise comparisons and noticed that the same…

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KEGG T02994: 18603710

Entry 18603710          CDS       T02994                                  Name (RefSeq) gibberellin 2-beta-dioxygenase 2   KO K04125   gibberellin 2beta-dioxygenase [EC:1.14.11.13] Organism tcc  Theobroma cacao (cacao) Pathway tcc00904   Diterpenoid biosynthesis tcc01110   Biosynthesis of secondary metabolites Brite KEGG Orthology (KO) [BR:tcc00001] 09100 Metabolism  09109 Metabolism of terpenoids and polyketides   00904 Diterpenoid biosynthesis    18603710Enzymes [BR:tcc01000] 1. Oxidoreductases  1.14  Acting on paired donors, with incorporation or reduction of molecular oxygen   1.14.11  With…

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all(rownames(cts) %in% txdf$TXNAME) is FALSE in DTU Analysis in R

Good afternoon, I am trying to do a DTU analysis for my research, but I am kinda new to this stuff and I have some problems. In particular on point 5). I am following the workflow of Bioconductor vignette rnaseqDTU and my pipeline is this: 1) read salmon quants ##…

Continue Reading all(rownames(cts) %in% txdf$TXNAME) is FALSE in DTU Analysis in R

KEGG T01028: 712850

Entry 712850            CDS       T01028                                  Symbol PDE4A Name (RefSeq) cAMP-specific 3′,5′-cyclic phosphodiesterase 4A isoform X1   KO K13293   cAMP-specific phosphodiesterase 4 [EC:3.1.4.53] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc00230   Purine metabolism mcc01100   Metabolic pathways mcc04024   cAMP signaling pathway mcc04928   Parathyroid hormone synthesis, secretion and action mcc05032   Morphine addiction Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism  09104…

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KEGG T01028: 701317

Entry 701317            CDS       T01028                                  Symbol HIPK4 Name (RefSeq) homeodomain-interacting protein kinase 4   KO K08826   homeodomain interacting protein kinase [EC:2.7.11.1] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc04218   Cellular senescence Brite KEGG Orthology (KO) [BR:mcc00001] 09140 Cellular Processes  09143 Cell growth and death   04218 Cellular senescence    701317 (HIPK4) 09180 Brite Hierarchies  09181 Protein families: metabolism   01001 Protein kinases [BR:mcc01001]    701317 (HIPK4)Enzymes [BR:mcc01000] 2….

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KEGG T01028: 717212

Entry 717212            CDS       T01028                                  Symbol PPT2 Name (RefSeq) lysosomal thioesterase PPT2 isoform X1   KO K01074   palmitoyl-protein thioesterase [EC:3.1.2.22] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc00062   Fatty acid elongation mcc01100   Metabolic pathways mcc01212   Fatty acid metabolism mcc04142   Lysosome Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism  09103 Lipid metabolism   00062 Fatty acid elongation    717212 (PPT2) 09140 Cellular Processes  09141 Transport…

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KEGG T01028: 715211

Entry 715211            CDS       T01028                                  Symbol CYB5RL Name (RefSeq) NADH-cytochrome b5 reductase-like isoform X1   KO K00326   cytochrome-b5 reductase [EC:1.6.2.2] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc00520   Amino sugar and nucleotide sugar metabolism Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism  09101 Carbohydrate metabolism   00520 Amino sugar and nucleotide sugar metabolism    715211 (CYB5RL)Enzymes [BR:mcc01000] 1. Oxidoreductases  1.6  Acting on NADH or NADPH   1.6.2  With…

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KEGG T01028: 705628

Entry 705628            CDS       T01028                                  Symbol NUP85 Name (RefSeq) nuclear pore complex protein Nup85 isoform X1   KO K14304   nuclear pore complex protein Nup85 Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc03013   Nucleocytoplasmic transport mcc05014   Amyotrophic lateral sclerosis Brite KEGG Orthology (KO) [BR:mcc00001] 09120 Genetic Information Processing  09122 Translation   03013 Nucleocytoplasmic transport    705628 (NUP85) 09160 Human Diseases  09164 Neurodegenerative disease   05014 Amyotrophic…

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KEGG T01028: 717394

Entry 717394            CDS       T01028                                  Symbol VPS35 Name (RefSeq) vacuolar protein sorting-associated protein 35 isoform X1   KO K18468   vacuolar protein sorting-associated protein 35 Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc04144   Endocytosis Brite KEGG Orthology (KO) [BR:mcc00001] 09140 Cellular Processes  09141 Transport and catabolism   04144 Endocytosis    717394 (VPS35) 09180 Brite Hierarchies  09182 Protein families: genetic information processing   04131 Membrane trafficking [BR:mcc04131]    717394…

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Comment: Map genome positions onto protein coordinates?

You need to get the geneID first. For PDB structures, you may be able to retrieve it from RCSB PDB APIs. For AlphaFold UniProt IDs, you can do this way: `url = “rest.uniprot.org/uniprotkb/search?format=json&fields=xref_geneid,gene_names&query=&#8221; + structure; let geneData = await me.getAjaxPromise(url, ‘json’); let geneId = (geneData.results[0] && geneData.results[0].uniProtKBCrossReferences && geneData.results[0].uniProtKBCrossReferences[0]) ?…

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Mouse mm10 chr4:22,481,383-22,489,763 UCSC Genome Browser v455

     Custom Tracks Adiposehidedensesquishpackfull Cerebellumhidedensesquishpackfull Cortexhidedensesquishpackfull Liverhidedensesquishpackfull Lunghidedensesquishpackfull Sintesthidedensesquishpackfull Spleenhidedensesquishpackfull    mouse_7_core ATAC Adipose Rep1hidedensefull ATAC Adipose Rep2hidedensefull ATAC Cerebellum Rep1hidedensefull ATAC Cerebellum Rep2hidedensefull ATAC Colon Rep1hidedensefull ATAC Colon Rep2hidedensefull ATAC Cortex Rep1hidedensefull ATAC Cortex Rep2hidedensefull ATAC Heart Rep1hidedensefull ATAC Heart Rep2hidedensefull ATAC Liver Rep1hidedensefull ATAC Liver Rep2hidedensefull ATAC…

Continue Reading Mouse mm10 chr4:22,481,383-22,489,763 UCSC Genome Browser v455

How can I devise a method like DESeq2 to give statistics for paired multiple -omic datasets?

Hi, I am a PhD student seeking advice on how I can devise a method like DESeq2 to give statistics for paired multiple -omic datasets that are aligned with those produced on RNA-Seq count data by DESeq2 (one of the multi-omic datasets for paired samples), so that they can be…

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KEGG T00007: b1676

Entry b1676             CDS       T00007                                  Symbol pykF Name (RefSeq) pyruvate kinase I   KO K00873   pyruvate kinase [EC:2.7.1.40] Organism eco  Escherichia coli K-12 MG1655 Pathway eco00010   Glycolysis / Gluconeogenesis eco00620   Pyruvate metabolism eco01100   Metabolic pathways eco01110   Biosynthesis of secondary metabolites eco01120   Microbial metabolism in diverse environments eco01200   Carbon metabolism eco01230   Biosynthesis of amino acids Module…

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pyDESeq2 Index Error?

I was trying to do a DEG analysis using DESeq2 but keeps giving me InvalidIndexError when my index object shouldn’t be a problem running the pyDESeq2 package. Here is my code: counts = pd.read_csv(‘filename.csv’) counts = counts.set_index(‘GeneID’) counts = counts.T metadata = pd.DataFrame(zip(counts.index, [‘Ctr’,’Ctr’,’Ctr’,Ctr’, ‘KO’,’KO’,’KO’,’KO’, ‘C2′,’C2′,’C2′,’C2’], columns = [‘Sample’, ‘Condition’])…

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DESeq2: DESeqDataSetFromMatrix Error

Everything was running smoothly until I ran into the DESeqDataSetFromMatrix error. Error in DESeqDataSetFromMatrix(countData = Counts, colData = coldata, : ncol(countData) == nrow(colData) is not TRUE My code: Counts <- read.delim(“RiboTag_count_matrix_10-05-2023.csv”, header = TRUE, sep=”,”) Counts # dimension is 24421 rows x 13 columns; first column is GeneID Counts <-…

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KEGG T01028: 717963

Entry 717963            CDS       T01028                                  Symbol STIM1 Name (RefSeq) stromal interaction molecule 1 precursor   KO K16059   stromal interaction molecule 1 Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc04020   Calcium signaling pathway mcc04611   Platelet activation Brite KEGG Orthology (KO) [BR:mcc00001] 09130 Environmental Information Processing  09132 Signal transduction   04020 Calcium signaling pathway    717963 (STIM1) 09150 Organismal Systems  09151 Immune system   04611 Platelet activation    717963…

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KEGG T05149: 103473078

Entry 103473078         CDS       T05149                                  Symbol ppt1 Name (RefSeq) palmitoyl-protein thioesterase 1 isoform X1   KO K01074   palmitoyl-protein thioesterase [EC:3.1.2.22] Organism pret  Poecilia reticulata (guppy) Pathway pret00062   Fatty acid elongation pret01100   Metabolic pathways pret01212   Fatty acid metabolism pret04142   Lysosome Brite KEGG Orthology (KO) [BR:pret00001] 09100 Metabolism  09103 Lipid metabolism   00062 Fatty acid elongation    103473078 (ppt1) 09140 Cellular Processes  09141 Transport and…

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KEGG T05897: 110480856

Entry 110480856         CDS       T05897                                  Symbol AGA Name (RefSeq) N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase   KO K01444   N4-(beta-N-acetylglucosaminyl)-L-asparaginase [EC:3.5.1.26] Organism lsr  Lonchura striata domestica (Bengalese finch) Pathway lsr00511   Other glycan degradation lsr04142   Lysosome Brite KEGG Orthology (KO) [BR:lsr00001] 09100 Metabolism  09107 Glycan biosynthesis and metabolism   00511 Other glycan degradation    110480856 (AGA) 09140 Cellular Processes  09141 Transport and catabolism   04142 Lysosome    110480856 (AGA)Enzymes [BR:lsr01000] 3. Hydrolases  3.5  Acting on carbon-nitrogen bonds,…

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Converting from BED to SAF/GFF

I believe that SAF format use 1-based coordinates that are closed on both ends. Here is how I got this conclusion. First make some toy data. $ cat genome.fa >chr1 AATTCCGGAAAATTTTCCCCGGGGAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCC $ cat reads.fa >q1 AAAATTTTCCCCGGGGAAAAAAAAAAAAAAAAAACC Map reads to the genome: $ STAR –runMode genomeGenerate –genomeDir test_star –genomeFastaFiles genome.fa –genomeSAindexNbases…

Continue Reading Converting from BED to SAF/GFF

RefSeq: XP_024590519

LOCUS XP_024590519 142 aa linear MAM 18-APR-2018 DEFINITION glia maturation factor beta isoform X2 [Neophocaena asiaeorientalis asiaeorientalis]. ACCESSION XP_024590519 VERSION XP_024590519.1 DBLINK BioProject: PRJNA449518 DBSOURCE REFSEQ: accession XM_024734751.1 KEYWORDS RefSeq. SOURCE Neophocaena asiaeorientalis asiaeorientalis (Yangtze finless porpoise) ORGANISM Neophocaena asiaeorientalis asiaeorientalis Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria;…

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KEGG T08832: 125909104

Entry 125925080         CDS       T08832                                  Name (RefSeq) adenylosuccinate synthetase isozyme 2 isoform X1   KO K01939   adenylosuccinate synthase [EC:6.3.4.4] Organism puc  Panthera uncia (snow leopard) Pathway puc00230   Purine metabolism puc00250   Alanine, aspartate and glutamate metabolism puc01100   Metabolic pathways puc01232   Nucleotide metabolism puc01240   Biosynthesis of cofactors Module puc_M00049   Adenine ribonucleotide biosynthesis, IMP => ADP,ATP Brite KEGG…

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rna-seq analysis with Salmon – how to Import and summarize using tximport

Hi! I’m trying to do RNA-seq analysis using salmon and would like to have a matrix of read counts of 10 RNA fastq files. I installed salmon with bioconda, however, I can only find version : 0.8.1 even after ‘conda update salmon’. So I have been doing with version 0.8.1…

Continue Reading rna-seq analysis with Salmon – how to Import and summarize using tximport

RefSeq: XP_033346483

LOCUS XP_033346483 290 aa linear INV 16-APR-2020 DEFINITION COP9 signalosome complex subunit 7b isoform X1 [Bombus vosnesenskii]. ACCESSION XP_033346483 VERSION XP_033346483.1 DBLINK BioProject: PRJNA623919 DBSOURCE REFSEQ: accession XM_033490592.1 KEYWORDS RefSeq. SOURCE Bombus vosnesenskii ORGANISM Bombus vosnesenskii Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Anthophila;…

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KEGG T00123: EF1761

Entry EF1761            CDS       T00123                                  Symbol ftsE Name (RefSeq) cell division ATP-binding protein FtsE   KO K09812   cell division transport system ATP-binding protein Organism efa  Enterococcus faecalis V583 Pathway efa02010   ABC transporters Brite KEGG Orthology (KO) [BR:efa00001] 09130 Environmental Information Processing  09131 Membrane transport   02010 ABC transporters    EF1761 (ftsE) 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03036 Chromosome and associated…

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Calculating TPM from featureCounts output

Calculating TPM from featureCounts output 3 Hi all, Have a simple question but just want to double check I’m not doing something stupid. I have paired-end RNA-seq data for which I have used featureCounts to quantify raw counts. I now want to normalize using the TPM formula. I read this…

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identify DEGs across all conditions and per specific conditions

Hi, I am analyzing a bulk-RNAseq and I want to analyse the dataset using Deseq2. I am very confused so apologies if it’s a stupid question. My dataset has 12 samples (3 per condition). the conditions are: treatment and control and 2 time points (0hr, 12hrs). So I wanted to…

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Page not found at /GeneAnnotation/?id=Peq006601&type=Phalaenopsis

Page not found at /GeneAnnotation/?id=Peq006601&type=Phalaenopsis Using the URLconf defined in orchidbase5.urls, Django tried these URL patterns, in this order: ^admin/ ^rec_histone/$ [name=”main_algorithm”] Info_download/$ [name=”Info_download”] Sum_download/$ [name=”Sum_download”] example_download/$ [name=”example_download”] ^ ^$ [name=”home2020″] ^ ^geneinfo2022/ [name=”geneinfo2020″] ^ ^releaseSummary2022/ [name=”releaseSummary2020″] ^ ^orchidSpecies/ [name=”orchidSpecies”] ^ ^Contacts/ [name=”Contacts”] ^ ^Orchidbase4.0_user_guide/ [name=”Orchidbase4_user_guide”] ^ ^Orchidbase5.0_user_guide/ [name=”Orchidbase5_user_guide”] ^…

Continue Reading Page not found at /GeneAnnotation/?id=Peq006601&type=Phalaenopsis

How to change from gene_id to GeneID/EntrezID using R

How to change from gene_id to GeneID/EntrezID using R 0 Hello im currently doing a differential expression analysis and the identifiers im using are gene_id’s, but to do the GO enrichment analysis and the domain anotation i need to have them in GeneID which according to what I have investigated…

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Dryad | Data — Data for: RNA-Seq dataset of RBL-2H3 (RPKM)

README RNA-Seq data for RBL-2H3 cells. [1]Content Introduction: The coverage of each gene, expression of gene(RPKM), total number of reads that aligned to gene, the description of gene are provided in this analysis. [2]format description: RNA-Seq results are presented in xlsx table, named *.Gene.rpkm.xlsx, each independent sample correspond to a…

Continue Reading Dryad | Data — Data for: RNA-Seq dataset of RBL-2H3 (RPKM)

KEGG T01028: 713306

Entry 713306            CDS       T01028                                  Symbol GATM Name (RefSeq) glycine amidinotransferase, mitochondrial   KO K00613   glycine amidinotransferase [EC:2.1.4.1] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc00260   Glycine, serine and threonine metabolism mcc00330   Arginine and proline metabolism mcc01100   Metabolic pathways Module mcc_M00047   Creatine pathway Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism  09105 Amino acid metabolism   00260 Glycine, serine and…

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Using ExomeDepth for GRCH38 processed samples to call CNVs

The only difference would be the annotations, instead of using bedframes from data(genes.hg19) and data(exons.hg19) in ExomeDepth, I got them from the UCSC Table Browser for hg38 (genome.ucsc.edu/cgi-bin/hgTables). The only info they contain are: chromosome start end name ..and then run as before. Change bed.frame = exons.hg19 to the exon…

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ML tree inferred from multiple genes

Hi guys, I am working with a directory of approximately 3,000 trimmed protein alignment files. Every alignment is one single copy orthologue containing sequences of 7 species obtained by Orthofinder. In fasta headers, I have species name_geneID. I want to calculate the best substitution models and then infer a Maximum…

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KEGG T08457: 116690928

Entry 116690928         CDS       T08457                                  Name (RefSeq) Krueppel-like factor 10   KO K09209   krueppel-like factor 10/11 Organism esp  Etheostoma spectabile (orangethroat darter) Brite KEGG Orthology (KO) [BR:esp00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03000 Transcription factors [BR:esp03000]    116690928Transcription factors [BR:esp03000] Eukaryotic type  Zinc finger   Cys2His2 SP/KLF family and related proteins    116690928 BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif Pfam:  zf-H2C2_2 zf-C2H2…

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RefSeq: XP_007448290

LOCUS XP_007448290 260 aa linear MAM 01-APR-2014 DEFINITION PREDICTED: alpha-ketoglutarate-dependent dioxygenase alkB homolog 2 isoform X1 [Lipotes vexillifer]. ACCESSION XP_007448290 VERSION XP_007448290.1 DBLINK BioProject: PRJNA232751 DBSOURCE REFSEQ: accession XM_007448228.1 KEYWORDS RefSeq. SOURCE Lipotes vexillifer (Yangtze River dolphin) ORGANISM Lipotes vexillifer Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla;…

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KEGG T01053: 5572547

Entry 5572547           CDS       T01053                                  Name (RefSeq) alanine aminotransferase 1   KO K00814   alanine transaminase [EC:2.6.1.2] Organism aag  Aedes aegypti (yellow fever mosquito) Pathway aag00220   Arginine biosynthesis aag00250   Alanine, aspartate and glutamate metabolism aag01100   Metabolic pathways aag01200   Carbon metabolism aag01210   2-Oxocarboxylic acid metabolism aag01230   Biosynthesis of amino acids Brite KEGG Orthology (KO) [BR:aag00001] 09100 Metabolism  09105 Amino…

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RefSeq: XP_026912832

LOCUS XP_026912832 160 aa linear MAM 04-APR-2023 DEFINITION protein FAM162B isoform X3 [Acinonyx jubatus]. ACCESSION XP_026912832 VERSION XP_026912832.1 DBLINK BioProject: PRJNA923316 DBSOURCE REFSEQ: accession XM_027057031.2 KEYWORDS RefSeq. SOURCE Acinonyx jubatus (cheetah) ORGANISM Acinonyx jubatus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Carnivora; Feliformia; Felidae; Acinonychinae; Acinonyx. COMMENT MODEL…

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KEGG T01001: 3202

Entry 3202              CDS       T01001                                  Symbol HOXA5, HOX1, HOX1.3, HOX1C Name (RefSeq) homeobox A5   KO K09305   homeobox protein HoxA/B/C5 Organism hsa  Homo sapiens (human) Brite KEGG Orthology (KO) [BR:hsa00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03000 Transcription factors [BR:hsa03000]    3202 (HOXA5)Transcription factors [BR:hsa03000] Eukaryotic type  Helix-turn-helix   Homeo domain ANTP: HOXL    3202 (HOXA5) BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif Pfam: …

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RefSeq: NP_001154929

LOCUS NP_001154929 155 aa linear ROD 03-MAY-2023 DEFINITION core-binding factor subunit beta isoform 3 [Mus musculus]. ACCESSION NP_001154929 VERSION NP_001154929.1 DBSOURCE REFSEQ: accession NM_001161457.1 KEYWORDS RefSeq. SOURCE Mus musculus (house mouse) ORGANISM Mus musculus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus;…

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KEGG T05885: 111164139

Entry 111179094         CDS       T05885                                  Symbol ADH1C Name (RefSeq) alcohol dehydrogenase 1C isoform X1   KO K13951   alcohol dehydrogenase 1/7 [EC:1.1.1.1] Organism dle  Delphinapterus leucas (beluga whale) Pathway dle00010   Glycolysis / Gluconeogenesis dle00071   Fatty acid degradation dle00350   Tyrosine metabolism dle00620   Pyruvate metabolism dle00830   Retinol metabolism dle00980   Metabolism of xenobiotics by cytochrome P450 dle00982   Drug metabolism…

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RefSeq: XP_007166569

LOCUS XP_007166569 140 aa linear MAM 27-JUN-2023 DEFINITION profilin-1 [Balaenoptera acutorostrata]. ACCESSION XP_007166569 VERSION XP_007166569.1 DBLINK BioProject: PRJNA986088 DBSOURCE REFSEQ: accession XM_007166507.3 KEYWORDS RefSeq. SOURCE Balaenoptera acutorostrata (minke whale) ORGANISM Balaenoptera acutorostrata Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Whippomorpha; Cetacea; Mysticeti; Balaenopteridae; Balaenoptera. COMMENT MODEL REFSEQ:…

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RefSeq: XP_024597028

LOCUS XP_024597028 208 aa linear MAM 18-APR-2018 DEFINITION protein THEM6 [Neophocaena asiaeorientalis asiaeorientalis]. ACCESSION XP_024597028 VERSION XP_024597028.1 DBLINK BioProject: PRJNA449518 DBSOURCE REFSEQ: accession XM_024741260.1 KEYWORDS RefSeq. SOURCE Neophocaena asiaeorientalis asiaeorientalis (Yangtze finless porpoise) ORGANISM Neophocaena asiaeorientalis asiaeorientalis Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Whippomorpha; Cetacea; Odontoceti;…

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KEGG T07554: 122421214

Entry 122453084         CDS       T07554                                  Name (RefSeq) 14-3-3 protein zeta/delta-like   KO K16197   14-3-3 protein beta/theta/zeta Organism ccad  Cervus canadensis (wapiti) Pathway ccad04110   Cell cycle ccad04114   Oocyte meiosis ccad04151   PI3K-Akt signaling pathway ccad04390   Hippo signaling pathway ccad05160   Hepatitis C ccad05161   Hepatitis B ccad05203   Viral carcinogenesis Brite KEGG Orthology (KO) [BR:ccad00001] 09130 Environmental Information Processing  09132 Signal transduction   04390…

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RefSeq: XP_013985108

LOCUS XP_013985108 229 aa linear VRT 07-JAN-2022 DEFINITION esterase OVCA2 isoform X1 [Salmo salar]. ACCESSION XP_013985108 VERSION XP_013985108.1 DBLINK BioProject: PRJNA788898 DBSOURCE REFSEQ: accession XM_014129633.2 KEYWORDS RefSeq. SOURCE Salmo salar (Atlantic salmon) ORGANISM Salmo salar Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Salmoninae; Salmo. COMMENT…

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KEGG T04128: 106353589

Entry 106400728         CDS       T04128                                  Name (RefSeq) eukaryotic translation initiation factor 2 subunit alpha homolog   KO K03237   translation initiation factor 2 subunit 1 Organism bna  Brassica napus (rape) Pathway bna04141   Protein processing in endoplasmic reticulum Brite KEGG Orthology (KO) [BR:bna00001] 09120 Genetic Information Processing  09123 Folding, sorting and degradation   04141 Protein processing in endoplasmic reticulum    106400728 09180 Brite Hierarchies  09182…

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KEGG T04128: 106349546

Entry 111211405         CDS       T04128                                  Name (RefSeq) transcription initiation factor TFIID subunit 4-like isoform X1   KO K03129   transcription initiation factor TFIID subunit 4 Organism bna  Brassica napus (rape) Pathway bna03022   Basal transcription factors Brite KEGG Orthology (KO) [BR:bna00001] 09120 Genetic Information Processing  09121 Transcription   03022 Basal transcription factors    111211405 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03021 Transcription machinery…

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KEGG T04128: 106353725

Entry 106430390         CDS       T04128                                  Name (RefSeq) splicing factor U2af large subunit B isoform X1   KO K12837   splicing factor U2AF 65 kDa subunit Organism bna  Brassica napus (rape) Pathway bna03040   Spliceosome Brite KEGG Orthology (KO) [BR:bna00001] 09120 Genetic Information Processing  09121 Transcription   03040 Spliceosome    106430390 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03041 Spliceosome [BR:bna03041]    106430390Spliceosome [BR:bna03041] Complex A  U2 snRNP components   U2…

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KEGG T01001: 6419

Entry 6419              CDS       T01001                                  Symbol SETMAR, METNASE, Mar1 Name (RefSeq) SET domain and mariner transposase fusion gene   KO K11433   [histone H3]-lysine36 N-dimethyltransferase SETMAR [EC:2.1.1.357] Organism hsa  Homo sapiens (human) Pathway hsa00310   Lysine degradation hsa01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:hsa00001] 09100 Metabolism  09105 Amino acid metabolism   00310 Lysine degradation    6419 (SETMAR) 09180 Brite Hierarchies  09182 Protein families: genetic…

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KEGG T04641: 108520276

Entry 108533396         CDS       T04641                                  Symbol SRSF6 Name (RefSeq) LOW QUALITY PROTEIN: serine/arginine-rich splicing factor 6   KO K12893   serine/arginine-rich splicing factor 4/5/6 Organism rbb  Rhinopithecus bieti (black snub-nosed monkey) Pathway rbb03040   Spliceosome rbb05168   Herpes simplex virus 1 infection Brite KEGG Orthology (KO) [BR:rbb00001] 09120 Genetic Information Processing  09121 Transcription   03040 Spliceosome    108533396 (SRSF6) 09160 Human Diseases  09172 Infectious disease: viral   05168…

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KEGG T01009: 100037961

Entry 396969            CDS       T01009                                  Symbol CTSH Name (RefSeq) pro-cathepsin H precursor   KO K01366   cathepsin H [EC:3.4.22.16] Organism ssc  Sus scrofa (pig) Pathway ssc04142   Lysosome ssc04210   Apoptosis Brite KEGG Orthology (KO) [BR:ssc00001] 09140 Cellular Processes  09141 Transport and catabolism   04142 Lysosome    396969 (CTSH)  09143 Cell growth and death   04210 Apoptosis    396969 (CTSH) 09180 Brite Hierarchies  09181 Protein families: metabolism   01002 Peptidases and inhibitors [BR:ssc01002]    396969…

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KEGG T04641: 108514704

Entry 108519261         CDS       T04641                                  Symbol HSD17B12 Name (RefSeq) very-long-chain 3-oxoacyl-CoA reductase   KO K10251   17beta-estradiol 17-dehydrogenase / very-long-chain 3-oxoacyl-CoA reductase [EC:1.1.1.62 1.1.1.330] Organism rbb  Rhinopithecus bieti (black snub-nosed monkey) Pathway rbb00062   Fatty acid elongation rbb00140   Steroid hormone biosynthesis rbb01040   Biosynthesis of unsaturated fatty acids rbb01100   Metabolic pathways rbb01212   Fatty acid metabolism Module rbb_M00415   Fatty…

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KEGG T04129: 105767858

Entry 105783514         CDS       T04129                                  Name (RefSeq) L-ascorbate oxidase homolog   KO K00423   L-ascorbate oxidase [EC:1.10.3.3] Organism gra  Gossypium raimondii Pathway gra00053   Ascorbate and aldarate metabolism gra01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:gra00001] 09100 Metabolism  09101 Carbohydrate metabolism   00053 Ascorbate and aldarate metabolism    105783514Enzymes [BR:gra01000] 1. Oxidoreductases  1.10  Acting on diphenols and related substances as donors   1.10.3  With oxygen as acceptor    1.10.3.3  L-ascorbate oxidase     105783514 BRITE…

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KEGG T01001: 3081

Entry 3081              CDS       T01001                                  Symbol HGD, AKU, HGO Name (RefSeq) homogentisate 1,2-dioxygenase   KO K00451   homogentisate 1,2-dioxygenase [EC:1.13.11.5] Organism hsa  Homo sapiens (human) Pathway hsa00350   Tyrosine metabolism hsa01100   Metabolic pathways Module hsa_M00044   Tyrosine degradation, tyrosine => homogentisate Network nt06016  Phenylalanine and tyrosine metabolism   Element N00708   Tyrosine degradation Disease H00163   Alkaptonuria Brite KEGG Orthology (KO) [BR:hsa00001] 09100…

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KEGG T08872: 112390697

Entry 112393175         CDS       T08872                                  Symbol RPL4 Name (RefSeq) 60S ribosomal protein L4   KO K02930   large subunit ribosomal protein L4e Organism nasi  Neophocaena asiaeorientalis asiaeorientalis (Yangtze finless porpoise) Pathway nasi03010   Ribosome nasi05171   Coronavirus disease – COVID-19 Brite KEGG Orthology (KO) [BR:nasi00001] 09120 Genetic Information Processing  09122 Translation   03010 Ribosome    112393175 (RPL4) 09160 Human Diseases  09172 Infectious disease: viral   05171 Coronavirus disease…

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Heatmap legend position change

Hello, This is code that I am using to generate a heatmap: color_fun <- colorRamp2(c(-4, 0, 4), c(“red”, “black”, “green”)) df = read.csv(“RAT7basedlog2version2.csv”, header = T) df$Cluster = factor(df$Cluster, levels =c( “1”, “2”, “3”, “4”, “5”, “6”, “7”, “8”, “9”, “10”, “11”, “12”, “13”, “14”, “15”, “16”, “17”, “18”, “19”,…

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KEGG T04894: 105026601

Entry 105026601         CDS       T04894                                  Name (RefSeq) catalase-like isoform X1   KO K03781   catalase [EC:1.11.1.6] Organism els  Esox lucius (northern pike) Pathway els00380   Tryptophan metabolism els00630   Glyoxylate and dicarboxylate metabolism els01100   Metabolic pathways els01200   Carbon metabolism els04068   FoxO signaling pathway els04146   Peroxisome Brite KEGG Orthology (KO) [BR:els00001] 09100 Metabolism  09101 Carbohydrate metabolism   00630 Glyoxylate and dicarboxylate metabolism    105026601  09105 Amino…

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KEGG T01001: 4522

Entry 4522              CDS       T01001                                  Symbol MTHFD1, CIMAH, MTHFC, MTHFD Name (RefSeq) methylenetetrahydrofolate dehydrogenase, cyclohydrolase and formyltetrahydrofolate synthetase 1   KO K00288   methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase / formyltetrahydrofolate synthetase [EC:1.5.1.5 3.5.4.9 6.3.4.3] Organism hsa  Homo sapiens (human) Pathway hsa00670   One carbon pool by folate hsa01100   Metabolic pathways hsa01240   Biosynthesis of cofactors Module hsa_M00141  …

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