User: kanwarjag

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kanwarjag770
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Posts by kanwarjag

<prev • 285 results • page 1 of 29 • next >
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Comment: C: representing pathways at different time points
... Thanks for the suggestion. The figure with heatmap and bar diagram in your previous post @ https://www.biostars.org/p/198414/#198416 shows % of genes in particular pathway. This % is for each pathway enrichment. What I want to explain is e.g my data has 20 of 100 apoptosis pathway genes so that me ...
written 7 days ago by kanwarjag770
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representing pathways at different time points
... For an RNAseq time points data - control, 1, 2 , 4 days I separately did pathway analysis and has pathway enriched along with -log10 (p) in the form of bar diagrams. I have selected some pathways that are common in at least two time points while there are few pathways that are only in last time po ...
rna-seq written 7 days ago by kanwarjag770 • updated 7 days ago by Alex Reynolds20k
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RNA seq and promoter consensus sequence
... I have a rat RNA-seq data I want to check in 1000 bp upstream of TSS of these genes a common consensus sequence. Is there ant tool that may help me directly to find TSS from gene list and screen in -1000 bp of TSS to identify consensus sequence. Thanks ...
rna-seq written 11 days ago by kanwarjag770 • updated 11 days ago by shoujun.gu220
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circos plot gene expression by RNA-Seq
... Is it possible to show differential expression of genes using RNA seq by circos plot? Are there any specific guidelines or instructions to follow , I could not find anything specific for expression on Circos web page for expression. Thanks ...
circos plot rna-seq written 14 days ago by kanwarjag770 • updated 13 days ago by bernatgel770
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retrieving sequences of a upstream and downstream of a coordinate for hg19
... I have location of peak summit from my chipseq data and want to extract sequences 500 bp upstream and downstream of this coordinate from hg19. What should be easieast approach. Apology for a naive question, but I could not recollect or find on net how I used to do this. Thanks ...
chip-seq written 16 days ago by kanwarjag770 • updated 16 days ago by ATPoint1.1k
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finding common Chip-seq motif from different species
... I have a TF and am checking its enrichment across human (main aim) mouse and Rat public datasets. I have identified genes (homologous) and has a list of binding peaks. Now if I have to find a common binding motif what should be my approach should I take seq corresponding to respective genomes combi ...
chip-seq written 18 days ago by kanwarjag770
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gtf file for xenopus tropcalis
... Where can I find a gtf file of xenopus tropicalis compatible with Hisat/ Tophat? Thanks Kanwar ...
rna-seq written 18 days ago by kanwarjag770 • updated 18 days ago by genomax33k
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survival curve on expression of two combined genes
... Is there any online web based tool that can allow me to draw survival curve of the basis of expression of two genes together vs each gene. We can either use TCGA data or just array expression data. Thanks ...
kaplam meir rna-seq written 26 days ago by kanwarjag770
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Fibrosarcoma database for mRNA expression
... Is there a database that has expression data of fibrosarcoma- RNA-seq or array either one should work. Thanks ...
mrna expression fibrosarcome written 4 weeks ago by kanwarjag770 • updated 4 days ago by Biostar ♦♦ 20
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Comment: C: An enriched gene in GSEA
... There is a gene X we found to be associated with a particular pathway after GSEA. However a search of literature and GSEA datasets do not have the said gene. But that gene is present in our differentially expressed genes. ...
written 4 months ago by kanwarjag770

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