Find top genes that correlate with my gene of interest using TCGA RNA-Seq data and CCLE data in R.

Question

[dila5458451]

Hi - I'm new here.

I know some basics i R. I want to use R to find the top genes whose expression correlates with my gene of interest using TCGA RNA-Seq datasets and CCLE datasets to generate a figure depicting the correlation.

Any ideas on where to begin with this?

THIS IS EMERGENT ...PLEASE HELP ME

ANY REF CODE will be helpful thanks

Answer 1

[Kevin Blighe]

For TCGA, try GEPIA (see Multiple Gene Analysis):

• http://gepia.cancer-pku.cn/

For CCLE, I have a tutorial here:

• https://github.com/kevinblighe/AunerLab_CCLE

There are likely other solutions that are readily-available via a web browser - please try a search in Google.

Kevin

[dila5458451]

but it need to be done in R how can ı download tcga pancan data set

[dila5458451]

Actually, I download tcga data with tcgabiolinks but the data need further analysis first because it is raw data. So I need to download rpkm tcga data

[dila5458451]

also I look your ccle tutorials ı don't see thre is no data named CCLE_RNAseq_genes_rpkm_20180929.gct.gz or Cell_lines_annotations_20181226 Can you help me? What data should I download and use ?

[Kevin Blighe]

You need to take whichever is the most recent data. The files are date-stamped. The file CCLE_RNAseq_genes_rpkm_20180929.gct.gz, for example, is from 2018-09-29 (September 29, 2018).

[dila5458451]

there is data called CCLE_RNAseq_reads.csv or CCLE_RNAseq_transcripts.csv which one I should use