We have done RNAseq to unknown tumors in chicken. They tumors are are likely to be lymphoid tumors. I want to identify the tumor cell of origin (B-cell, T-cell, dendritic cell, macrophage,...). I tried 2 approaches: 1) I Identified 262 annotated genes with high FPKM ( > 200 as an arbitrary cut off) then I did pathway enrichment analysis using the available orthogonal genes in human (only 244 out of the initial 262). I did not have any pathognomonic signature, The lymphoid makers appears only in the low covered genes (FPKM <100). The group of gene of high coverage has a large no of ribosomal proteins. Any suggestions on this will be appreciated.
2) The second approach I tried was my trial to implement the "DeconRNASeq" R package (http://www.bioconductor.org/packages/2.12/bioc/html/DeconRNASeq.html) The package requires an expected expression profile of every cell type suspected to be seen in the heterogeneous tumor tissue. Is there a source of such expression profiles from different primary immune cells?
Thank you
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drtamermansour •
What I managed to do (for human cancer samples) is to get microarray data for various tissues (RNA-Seq-based illumine body map could also be used) and do a correlation analysis. Surprisingly, the correlations have shown clearly whether the tumor sample was from breast or prostate cancer. So I would recommend you get a list of well-annotated genes present on arrays for chicken and get FPKM for them. Then correlate log FPKM with log Intensity from arrays and see the closest tissue
is there a user-friendly data base to get these microarray data from specially for tumors ?
The best thing I know is to browse the good old GEO ( http://www.ncbi.nlm.nih.gov/geo/ ).
If you manage to get your hands on expression data such as mikhail suggested, I would have done PCA or hierarchical clustering based on gene expression.
Such techniques are easily implemented in R by most differential gene expression analysis packages, such as DESeq or EdgeR.
Cheers,
IV
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If you look in the pathology literature, is there a consensus on cell surface markers for your malignancy of interest? Even in blood tumors it's rare that expression is specific enough to determine the cell-of-origin when the possible candidates are closely related.