Tag: geneID

KEGG T00005: YNL036W

Entry YNL036W           CDS       T00005                                  Symbol NCE103, NCE3 Name (RefSeq) carbonate dehydratase NCE103   KO K01673   carbonic anhydrase [EC:4.2.1.1] Organism sce  Saccharomyces cerevisiae (budding yeast) Pathway sce00910   Nitrogen metabolism sce01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:sce00001] 09100 Metabolism  09102 Energy metabolism   00910 Nitrogen metabolism    YNL036W (NCE103)Enzymes [BR:sce01000] 4. Lyases  4.2  Carbon-oxygen lyases   4.2.1  Hydro-lyases    4.2.1.1  carbonic anhydrase     YNL036W (NCE103) BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif Pfam: …

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UCSC Genome Browser | Encyclopedia MDPI

1. History Initially built and still managed by Jim Kent, then a graduate student, and David Haussler, professor of Computer Science (now Biomolecular Engineering) at the University of California, Santa Cruz in 2000, the UCSC Genome Browser began as a resource for the distribution of the initial fruits of the…

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[SOLVED] Special .bed to .fa conversion (GenomicCoordinates/DNAsequence) ~ Linux Fixes

My aim is to create a custom protein sequence reference file (protein.fa) from genomic coordinates (origin.bed). (origin.bed; with Chromosome, start, end, TranscriptID, strand, GeneID) chr1 109202569 109202584 ENST00000370031.1_uORF_0 – ENSG00000162639.11 chr1 109203584 109203617 ENST00000370031.1_uORF_0 – ENSG00000162639.11 chr11 102188276 102188302 ENST00000263464.3_uORF_0 + ENSG00000023445.9 chr11 10830291 10830306 ENST00000530211.1_uORF_1 – ENSG00000110321.11 chr11 10830400…

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KEGG T01001: 4171

Entry 4171              CDS       T01001                                  Symbol MCM2, BM28, CCNL1, CDCL1, D3S3194, DFNA70, MITOTIN, cdc19 Name (RefSeq) minichromosome maintenance complex component 2   KO K02540   DNA replication licensing factor MCM2 [EC:5.6.2.3] Organism hsa  Homo sapiens (human) Pathway hsa03030   DNA replication hsa04110   Cell cycle Disease H00604   Deafness, autosomal dominant Brite KEGG Orthology (KO) [BR:hsa00001] 09120 Genetic Information Processing  09124…

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KEGG T02666: 101290786

Entry 101298727         CDS       T02666                                  Name (RefSeq) triacylglycerol lipase SDP1   KO K14674   TAG lipase / steryl ester hydrolase / phospholipase A2 / LPA acyltransferase [EC:3.1.1.3 3.1.1.13 3.1.1.4 2.3.1.51] Organism fve  Fragaria vesca (woodland strawberry) Pathway fve00100   Steroid biosynthesis fve00561   Glycerolipid metabolism fve00564   Glycerophospholipid metabolism fve00565   Ether lipid metabolism fve00590   Arachidonic acid metabolism fve00591   Linoleic…

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How can I convert Ensembl ID to gene symbol in R?

I tried several R packages (mygene, org.Hs.eg.db, biomaRt, EnsDb.Hsapiens.v79) to convert Ensembl.gene to gene.symbol, and found that the EnsDb.Hsapiens.v79 package / gene database provides the best conversion quality (in terms of being able to convert most of Ensembl.gene to gene.symbol). Install the package if you have not installed by running…

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GJA5 Polyclonal Antibody | APR27223N | Leading Biology

Brand Leading Biology Catalog Number APR27223N Product Type Polyclonal Antibodies Field of Research Cell Biology & Developmental Biology>Cell Adhesion …

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KEGG T01015: 107278078

Entry 4330855           CDS       T01015                                  Name (RefSeq) auxin-responsive protein SAUR32   KO K14488   SAUR family protein Organism osa  Oryza sativa japonica (Japanese rice) (RefSeq) Pathway osa04075   Plant hormone signal transduction Brite KEGG Orthology (KO) [BR:osa00001] 09130 Environmental Information Processing  09132 Signal transduction   04075 Plant hormone signal transduction    4330855 BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif Pfam:  Auxin_inducible Motif Other DBs…

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Python pandas transforming int to float in gff subsetting

Hey guys, I’ve written this python code. import pandas as pd from Bio import SeqIO import argparse parser= argparse.ArgumentParser(add_help=False) parser.add_argument(“-h”, “–help”, action=”help”, default=argparse.SUPPRESS, help= “Get partial gff given a pattern on Names field”) parser.add_argument(“-g”, help= “-g: gff file”, required = “True”) parser.add_argument(“-l”, help= “-l: list of patterns to search on…

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UniProt: A0A6I9ZUN5_ACIJB

ID A0A6I9ZUN5_ACIJB Unreviewed; 234 AA. AC A0A6I9ZUN5; DT 07-OCT-2020, integrated into UniProtKB/TrEMBL. DT 07-OCT-2020, sequence version 1. DT 25-MAY-2022, entry version 6. DE SubName: Full=tumor necrosis factor ligand superfamily member 8 {ECO:0000313|RefSeq:XP_014931799.1}; GN Name=TNFSF8 {ECO:0000313|RefSeq:XP_014931799.1}; OS Acinonyx jubatus (Cheetah). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Laurasiatheria;…

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can gff2 reference used in htseq-count?

Dear all We are recently working with E.coli plasmid and tried to summarize the gene counts from our RNA-Seq samples. The short reads were mapped to E.coli plasmid using tophat which generated bam files accordingly. However, we were unable to obtain a gff3 version of our target plasmid genome, the…

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KEGG T01003: 286761

Entry 286761            CDS       T01003                                  Symbol Vcpip1 Name (RefSeq) deubiquitinating protein VCPIP1   KO K11861   deubiquitinating protein VCIP135 [EC:3.4.19.12] Organism rno  Rattus norvegicus (rat) Brite KEGG Orthology (KO) [BR:rno00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01002 Peptidases and inhibitors [BR:rno01002]    286761 (Vcpip1)  09182 Protein families: genetic information processing   04121 Ubiquitin system [BR:rno04121]    286761 (Vcpip1)Enzymes [BR:rno01000] 3. Hydrolases  3.4  Acting on peptide bonds (peptidases)   3.4.19  Omega peptidases    3.4.19.12  ubiquitinyl…

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Unsuccessful DE analysis using limma

This might be a bit long, please bare with me. I’m conducting a differential expression analysis using limma – voom. My comparison is regarding response vs non-response to a cancer drug. However, I’m not getting any DE genes, absolute zeros. Someone here once recommended not to use contrast matrix for…

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use gene symbol in heatmap instead of ensemble geneID

Hi All I plot the heat map for my logCPM successfully but using Ensemble geneIDs. I need the heatmap to have the gene symbols, I can convert the ensemble gene IDs to gene IDs fine, but don’t know how to reflect this on the heatmap. My code for the heatmap…

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r – convert ALL genes from ensembl ID to symbol without NAs

I tried to convert genes with ensembl ID to Symbol I used the “EnsDb.Hsapiens.v86” package using this code: library(“EnsDb.Hsapiens.v86”) mapIds <- mapIds(EnsDb.Hsapiens.v86, keys = genes, keytype = “GENEID”, column = “SYMBOL”) mapIds Results is like that: ENSG00000033327 GAB2 ENSG00000033627 ATP6V0A1 ENSG00000033800 PIAS1 ENSG00000033867 SLC4A7 ENSG00000034063 < NA > ENSG00000034152 MAP2K3…

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Separate exogenous from endogenous transcripts using Salmon RNAseq DTU

Dear friends, We are trying to use Salmon for DTU analysis. We want to separate exogenous from endogenous transcripts by following this post www.biostars.org/p/443701/ and this paper f1000research.com/articles/7-952 We are focusing on a gene called ASCL1 (endo-ASCL1). We transduced cells with lentiviral vector containing ASCL1 ORF only (Lenti-ASCL1). There should…

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Human GSTO2 shRNA Plasmid | Abbexa Ltd

Price: €675.00 (Size: 150 µg) Click on the image to see the image legend shRNA Plasmid to inhibit GSTO2 expression by RNA interference. This product contains 3 separate slightly different shRNA sequences which knock down human GSTO2 gene specifically. Each vial contains 50 μg of lyophilized shRNA. Target GSTO2 Reactivity…

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Pathway analysis of RNAseq data using goseq package

Hello, I have finished the RNA seq analysis and I am trying to perform some pathway analysis. I have used the gage package and I was looking online about another package called goseq that takes into account length bias. However, when I run the code I get an error. How…

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Efficient way of mapping UniProt IDs to representative UniRef90 IDs?

You can do this directly on UniProt: www.uniprot.org/uploadlists/ Just paste or upload your list of UniProt IDs, and select “UniProtKB AC/ID” in the “From” field and “UniParc” in the “To” field I’ve also written a script, pasted below, that can do this with some useful options: $ uniprot_map.pl -h uniprot_map.pl…

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KEGG T01001: 5105

Entry 5106              CDS       T01001                                  Symbol PCK2, PEPCK, PEPCK-M, PEPCK2 Name (RefSeq) phosphoenolpyruvate carboxykinase 2, mitochondrial   KO K01596   phosphoenolpyruvate carboxykinase (GTP) [EC:4.1.1.32] Organism hsa  Homo sapiens (human) Pathway hsa00010   Glycolysis / Gluconeogenesis hsa00020   Citrate cycle (TCA cycle) hsa00620   Pyruvate metabolism hsa01100   Metabolic pathways hsa03320   PPAR signaling pathway hsa04068   FoxO signaling pathway hsa04151   PI3K-Akt signaling…

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rna seq – How does DESeq2 “collapseReplicates()” function work on read counts data?

Comparing read counts from an RNA-seq experiment for two select genes before and after using DESeq2’s collapseReplicates() and plotCounts() functions yields interesting results: Before collapseReplicates() and plotCounts(): Geneid foo1.1 foo1.2 foo2.1 foo2.2 bar1.1 bar1.2 bar2.1 bar2.2 baz1.1 baz1.2 baz2.1 baz2.2 baz3.1 baz3.2 WASH7P 6 5 0 2 1 1 8…

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UniProt: A0A1S3QEZ7_SALSA

ID A0A1S3QEZ7_SALSA Unreviewed; 104 AA. AC A0A1S3QEZ7; DT 12-APR-2017, integrated into UniProtKB/TrEMBL. DT 12-APR-2017, sequence version 1. DT 02-JUN-2021, entry version 11. DE SubName: Full=lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog isoform X2 {ECO:0000313|RefSeq:XP_014038412.1}; GN Name=LOC106591717 {ECO:0000313|RefSeq:XP_014038412.1}; OS Salmo salar (Atlantic salmon). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Actinopterygii;…

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RefSeq: XP_007190711

LOCUS XP_007190711 296 aa linear MAM 12-FEB-2019 DEFINITION reticulon-4-interacting protein 1, mitochondrial isoform X3 [Balaenoptera acutorostrata scammoni]. ACCESSION XP_007190711 VERSION XP_007190711.1 DBLINK BioProject: PRJNA237330 DBSOURCE REFSEQ: accession XM_007190649.2 KEYWORDS RefSeq. SOURCE Balaenoptera acutorostrata scammoni ORGANISM Balaenoptera acutorostrata scammoni Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Whippomorpha; Cetacea;…

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How to convert transcript-relative coordinates to genomic coordinates?

How to convert transcript-relative coordinates to genomic coordinates? 0 I have queried using Entrez Utilities (efetch: www.ncbi.nlm.nih.gov/books/NBK25499/) and obtained annotations for transcripts like the following: >Feature ref|NM_152486.3| 1 2557 gene gene SAMD11 gene_syn MRS gene_desc sterile alpha motif domain containing 11 db_xref GeneID:148398 db_xref HGNC:HGNC:28706 db_xref MIM:616765 How/what database should…

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KEGG T00007: b1542

Entry b4323             CDS       T00007                                  Symbol uxuB Name (RefSeq) D-mannonate oxidoreductase   KO K00040   fructuronate reductase [EC:1.1.1.57] Organism eco  Escherichia coli K-12 MG1655 Pathway eco00040   Pentose and glucuronate interconversions eco01100   Metabolic pathways Module eco_M00061   D-Glucuronate degradation, D-glucuronate => pyruvate + D-glyceraldehyde 3P Brite KEGG Orthology (KO) [BR:eco00001] 09100 Metabolism  09101 Carbohydrate metabolism   00040 Pentose and glucuronate interconversions    b4323 (uxuB)Enzymes…

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rna seq – How does DESeq2 “collapseReplicates” work on read counts data?

Comparing read counts from an RNA-seq experiment for a couple select genes before and after using DESeq2’s collapseReplicates function yields interesting results: Before: Geneid foo1.1 foo1.2 foo2.1 foo2.2 foo3.1 foo3.2 bar1.1 bar1.2 bar2.1 bar2.2 bar3.1 bar3.2 baz1.1 baz1.2 baz2.1 baz2.2 baz3.1 baz3.2 WASH7P 6 5 0 2 7 3 1…

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KEGG T01005: 453503

Entry 453503            CDS       T01005                                  Symbol SNX1 Name (RefSeq) sorting nexin-1 isoform X3   KO K17917   sorting nexin-1/2 Organism ptr  Pan troglodytes (chimpanzee) Pathway ptr04144   Endocytosis Brite KEGG Orthology (KO) [BR:ptr00001] 09140 Cellular Processes  09141 Transport and catabolism   04144 Endocytosis    453503 (SNX1) 09180 Brite Hierarchies  09182 Protein families: genetic information processing   04131 Membrane trafficking [BR:ptr04131]    453503 (SNX1)  09183 Protein families: signaling and cellular processes   04990…

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KINNEY_DNMT1_METHYLATION_TARGETS

Standard name KINNEY_DNMT1_METHYLATION_TARGETS Systematic name M2508 Brief description Hypomethylated genes in prostate tissue from mice carrying hypomorphic alleles of DNMT1 [GeneID=1786]. Full description or abstract Previous studies have shown that tumor progression in the transgenic adenocarcinoma of mouse prostate (TRAMP) model is characterized by global DNA hypomethylation initiated during early-stage…

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Combining RNA-Seq read counts from 2 lanes of the same sample (.txt file)

Hi, I have a question on combining read counts from 2 lanes of the same sample. I have a very large RNA-Seq dataset downloaded from the NCBI GEO. The data files are in the *.txt format and each sample with 2 lanes obtained from featureCounts. I would like to perform…

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Running htseq-count to “grab” long non coding gene_id names

Running htseq-count to “grab” long non coding gene_id names 0 hi all, new to bioinformatics. so bare with me.. I am trying find long non coding RNA from RNA-seq data. As i checked the human gtf file there are 2 different types of long non coding RNA, “lnc_RNA” and “lncRNA”,…

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number of GO terms in results

clusterProfiler: number of GO terms in results 0 I am working with a non-model organism. So I constructed TERM2GENE and TERM2NAME files and used enricher to run GO enrichment analysis. The code I used was below. Finally, I got 71 GO terms in the result. But actually, there are 99…

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geneiD-genetranscript annotations

Hello, Trying to generate a frame with 2 columns: transcript_id and gene_id, in LINUX (gtf from esembl) grep -P -o ‘ESNCAGd{11} Equus_caballus.EquCab3.0.104.gtf’ > ensecag.txt grep -P -o ‘ESNCATd{11} Equus_caballus.EquCab3.0.104.gtf’ > ensecat.txt wc -l enseca* # To see if both files have the same length They are not the same length:…

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does not contain a ‘gene’ attribute

htseq-count returns : does not contain a ‘gene’ attribute 1 Dear BIOSTAR community, I’m trying to make count matrix with htseq-count, htseq-count -s yes -t gene -i gene 01.sorted.sam annotation_cattle.gff > 01.txt even with –idattr=gene , it returns error: Error processing GFF file (line 1864255 of file annotation_cattle.gff): Feature gene-D1Y31_gp1…

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Circos plot with logfold change RNA seq data

I am new to circos plot analysis and have been trying to use the cyclize package. I want to display mRNA differential gene expression data based on data analyses of 8 libraries and links between their respective target genes. The dataset I am working with looks like this geneid baseMean…

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Combining 2 different depth RNA-seq data (DESeq2)

Hello, I have two RNA-seq data generated from Illumina Novaseq (same experimental design but different depth, 25M and 15M reads/sample for Run1 and Run2 respectively). The dateset look like this: Samples Condition Run Sample_1 A R1 Sample_2 B R1 Sample_3 A R1 Sample_4 B R1 Sample_5 A R1 Sample_6 B…

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Combining RNA-seq data from 2 experiments (DESeq2)

Hello, I have two RNA-seq data generated from Illumina Novaseq (same experimental design but different depth, 25M and 15M reads/sample for Run1 and Run2 respectively). The dateset look like this: Samples Condition Run Sample_1 A R1 Sample_2 B R1 Sample_3 A R1 Sample_4 B R1 Sample_5 A R1 Sample_6 B…

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How to colour points in cnetplot of clustprofiler?

I have a cnetplot from running enrichment with kegg using clusterprofiler. I have scores input as the fold change but for each gene in the plot they are not varying in colour to show their difference in the fold change score. My dataset is genes of entrez IDs and then…

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Answer: AnnotationHub::mapIds() cannot find existing ENSG (GEO supplemental data cross-r

Hi, a quick check on NCBI Gene reveals that the official symbol for this is *PRXL2C*, not *AAED1*. In this way, I would not have expected `org.Hs.eg.db` (using ‘recent’ annotation) to have it. However, I can see that `EnsDb.Hsapiens.v86` (older version) does [have it]. So, there must have been an…

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