User: jack

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jack760
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5 months ago
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Posts by jack

<prev • 146 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 19 months ago by jack760 • updated 19 months ago by Kevin Blighe45k
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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 19 months ago by jack760 • updated 19 months ago by Istvan Albert ♦♦ 80k
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Comment: C: How to extract known pathways from protein protein interaction network?
... Either entire or partial is fine. ...
written 20 months ago by jack760
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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 20 months ago by jack760
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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 23 months ago by jack760 • updated 23 months ago by geek_y9.8k
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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 23 months ago by jack760 • updated 23 months ago by EagleEye6.4k
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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 23 months ago by jack760 • updated 23 months ago by EagleEye6.4k
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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 2.0 years ago by jack760 • updated 2.0 years ago by Jean-Karim Heriche19k
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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 2.2 years ago by jack760 • updated 2.2 years ago by ivivek_ngs4.8k
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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 genome transcript ensembl written 2.2 years ago by jack760 • updated 9 months ago by zx87547.7k

Latest awards to jack

Great Question 18 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 ?
Great Question 18 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 18 months ago, created a question with more than 1,000 views. For What is the best human 3'-UTR annotation?
Good Question 18 months ago, asked a question that was upvoted at least 5 times. For what are the best resource to learn Linux bash scripting for Bioinformatics
Popular Question 18 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Popular Question 18 months ago, created a question with more than 1,000 views. For How to convert UCSC transcript(isforms) ids to Ensemble transcript ids?
Great Question 18 months ago, created a question with more than 5,000 views. For How much of human genome transcribe? How much of transcriptome are non-coding RNAs?
Appreciated 18 months ago, created a post with more than 5 votes. For what are the best resource to learn Linux bash scripting for Bioinformatics
Great Question 18 months ago, created a question with more than 5,000 views. For what are the best resource to learn Linux bash scripting for Bioinformatics
Popular Question 18 months ago, created a question with more than 1,000 views. For Where to get human 3'-UTR multiple sequence alignment ?
Popular Question 18 months ago, created a question with more than 1,000 views. For How to find GO file and do GO enrichment analysis ?
Popular Question 18 months ago, created a question with more than 1,000 views. For How to make heatmap more bright with proper color spectrum ?
Popular Question 18 months ago, created a question with more than 1,000 views. For what is the best gene ontology enrichment analysis package to include the pipeline
Popular Question 18 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 18 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Popular Question 19 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Popular Question 19 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Epic Question 19 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 22 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion

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