Sometimes I need to choose cell lines for gene expression and I do not have a fast way to find out which cell line is appropriate either I want the gene expressed or not. Could anyone recommend a website?
I dont know, whether I understand ur requirement completely. But Human protein atlas gives information about protein level expression data for several genes (for which antibodies are good enough) in tissues, pathologies and some cell lines. http://www.proteinatlas.org/
thanks a lot! altohugh it is not exaclty what I was looking for, it is going to be very useful! I wish there was a similar atlas for the cell lines
BioGPS has an excellent atlas for NCI60 and other cell lines, as well as various tissues.
Hi, maybe you can have a look in Genevestigator: www.genevestigator.com. It is a database with highly curated microarray experiment. You can there check what is the expression profile of a gene (for instance in various cell lines). If you need help with the tool, let me know. cheers
The UCSC genome browser ( http://genome.ucsc.edu/ ) contains a large set of expression data for ENCODE cell types (both RNA-Seq and expression arrays), raw data is available there and at corresponding GEO records.
for example:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCaltechRnaSeq
There are other data types for these cell types as well (Transcription Factor Binding, Histone Mods, DNaseI, 5C, ChIA-PET, etc).
Look under the Expression and Regulation sections of hg19 (GRCh37) in the browser.
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology