Dear all, I want to extract the genes related to colorectum but the database TIGER only showed the tissue view of colon. please suggest any database that can give the ESTs or expression profile of this tissue.
Thanks.
If you want to identify top expressed genes in normal colon.
- GTEX (https://www.gtexportal.org/home/). This portal allows users to obatin list of top 50 highly expressed genes in colon(sigmoid) or colon(transverse)
If you want to see top genes differentially expressed in colon adenocarcinoma (COAD) or rectal adenocarcinoma (READ) compared to normals from The cancer genome atlas database(TCGA)
- UALCAN (http://ualcan.path.uab.edu/analysis.html). This portal presents precompiled list of top 250 over-/under-expressed genes
Hi, adding to Darshan answer, If you are interested in the human gene expression profile then you can also check the human protein atlas:
https://www.proteinatlas.org/humanproteome/colon#colontranscriptome
Or for cancer cell lines BioGPS http://amp.pharm.mssm.edu/Harmonizome/dataset/BioGPS+Cell+Line+Gene+Expression+Profiles.
You can also use Expression Atlas from EMBL-EBI (contains also GTEx data). You can also specify for which type of colon cancer you want to see the expression and differential expression results from various comparisons
https://www.ebi.ac.uk/gxa/search?geneQuery=%5B%5D&organism=Homo%20sapiens&conditionQuery=%5B%7B"value"%3A"colon"%7D%5D&bs=%7B"homo%20sapiens"%3A%5B"ORGANISM_PART"%5D%7D#baseline
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