User: jack

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jack710
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710
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Posts by jack

<prev • 145 results • page 1 of 15 • next >
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How to exclude some of breast cancer subtypes just by looking at gene expression?
... Hi, Probably you all know about PAM50 gene signature for breast cancer sub typing. What I'm looking for is the some of small sets of the genes that their expression levels(expressed or not) helps me to exclude some of the breast cancer subtypes (For example, by looking at gene A and gene B expressi ...
genome gene rna-seq cancer written 7 months ago by jack710 • updated 7 months ago by Kevin Blighe24k
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How is it possible that multiple proteins maps to single transcript ids ?
... Hi all, I've downloaded transcript mapping to PDB annotation from [GENECODE][1] [1]: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.metadata.PDB.gz When I look at the table, i see that one transcript id maps to multiple proteins. I was pondering about the reason behind ...
chip-seq sequencing protein rna-seq bioinformatics written 7 months ago by jack710 • updated 7 months ago by Istvan Albert ♦♦ 77k
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Comment: C: How to extract known pathways from protein protein interaction network?
... Either entire or partial is fine. ...
written 8 months ago by jack710
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How to extract known pathways from protein protein interaction network?
... Hi, Given physical protein protein interaction like String and KEGG pathway. I would like to know how many of KEGG pathways or signaling pathways exist in PPI network. Is there any tool to extract known pathways(either entire or partial) from PPI network ? ...
pathway network protein written 8 months ago by jack710
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Computing TPM from normalized read count from DESEQ
... Hey all, I have normalised read count from DESeq2 for miRNA. I would like to compute TPM out of this normalised read count. I was wondering whether would it be possibile to do that ? ...
expression mirna deseq genomics rna-seq written 11 months ago by jack710 • updated 11 months ago by geek_y8.6k
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Looking for small RNA-seq in single cell
... Hey, I'm looking database that contains small RNA-seq for single cell. Is there any resource to download single cell small RNA-seq ? ...
genome rna-seq sequencing written 11 months ago by jack710 • updated 11 months ago by EagleEye5.5k
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How to do GO enrichment alanysis at isoform levels ?
... Hi, I would like to do Gene ontology enrichment analysis at isoform leveles(not gene levels). I have table that links each transcripts to SwissProt protein names as follows: ENST00000335137.3 Q8NH21 Q8NH21 ENST00000426406.2 Q6IEY1 Q6IEY1 ENST00000332831.3 Q6IEY1 Q6IEY1 ENST00000342 ...
genome bioinformatics network rna-seq ontology written 11 months ago by jack710 • updated 11 months ago by EagleEye5.5k
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How to map protein isoform IDs to transcripts IDs ?
... Hi, I would like to map my protein isoform IDs (refseq) to transcript ids. I was wondering whether can someone help me by that ? For example gene ZC3H14 produce following three different isoforms: ZC3H14 NP_079100.2,NP_001153575.1,NP_001313239.1 I would like to map this isoforms to the transcrip ...
proteomics genome rna-seq written 12 months ago by jack710 • updated 12 months ago by Jean-Karim Heriche16k
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Is they any R package to download processed miRNA expression levle from TCGA?
... Hi all, I would like to download processed miRNA expression levels for different cancers from TCGA. I was wondering whether is there any pakage such that I can use it to download data ? I tried to dowload maually from ICGC, but miRNAs are not annotated. I was wondering whether can you help me wit ...
bioinformatics tca next-gen rna-seq written 14 months ago by jack710 • updated 14 months ago by vchris_ngs4.5k
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What does *.* represent after Ensembl transcript name ?
... Hi all, I have expression level of trancripts and most of them contain a number after [.]. As example: ENST00000352998.3 When I search in Ensembl database, instead of **ENST00000352998.3** it shows me **ENST00000352998.7** Does this means that these two are two different transcripts ? or I can s ...
gene bioinformatics ensemble transcript genome written 15 months ago by jack710 • updated 15 months ago by agata88670

Latest awards to jack

Popular Question 6 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Popular Question 7 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Popular Question 7 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Epic Question 7 months ago, created a question with more than 10,000 views. For What is the simple way to remove known batch effect from RNA-seq data ?
Popular Question 10 months ago, created a question with more than 1,000 views. For How to convert UCSC transcript(isforms) ids to Ensemble transcript ids?
Popular Question 10 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Popular Question 10 months ago, created a question with more than 1,000 views. For Why FPKM value of gene expression profiles are very close to zero?
Popular Question 12 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
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Popular Question 13 months ago, created a question with more than 1,000 views. For Which kind of microRNAs expression are measured in TCGA?
Popular Question 14 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Popular Question 14 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Great Question 15 months ago, created a question with more than 5,000 views. For How to download Gene annotations.gtf file for Drosophila melanogaster
Popular Question 16 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Epic Question 16 months ago, created a question with more than 10,000 views. For What is the simple way to remove known batch effect from RNA-seq data ?
Great Question 17 months ago, created a question with more than 5,000 views. For What is the simple way to remove known batch effect from RNA-seq data ?
Popular Question 19 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Student 19 months ago, asked a question with at least 3 up-votes. For what are the best resource to learn Linux bash scripting for Bioinformatics
Great Question 20 months ago, created a question with more than 5,000 views. For What is the best programming language for NGS data analysis pipeline development?
Popular Question 22 months ago, created a question with more than 1,000 views. For How to detect and correct batch effect in NGS expression data ?
Popular Question 23 months ago, created a question with more than 1,000 views. For How to detect and correct batch effect in NGS expression data ?
Student 23 months ago, asked a question with at least 3 up-votes. For what are the best resource to learn Linux bash scripting for Bioinformatics

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