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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…
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…
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…
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 =…
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…
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…
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…
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…
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…
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”] ^…
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/…
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…
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…
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…
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…
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…
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…
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…
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…
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 –…
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…
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…
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…
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)…
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…
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)…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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 –…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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 ##…
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…
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….
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…
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…
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…
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…
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=” + structure; let geneData = await me.getAjaxPromise(url, ‘json’); let geneId = (geneData.results[0] && geneData.results[0].uniProtKBCrossReferences && geneData.results[0].uniProtKBCrossReferences[0]) ?…
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…
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…
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…
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’])…
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 <-…
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…
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…
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,…
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…
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;…
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…
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…
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;…
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…
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…
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…
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”] ^…
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…
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…
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…
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…
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…
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…
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;…
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…
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…
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: …
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;…
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…
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:…
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;…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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”,…
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…
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 …