Entering edit mode
10 months ago
Chris
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340
Hi Biostars,
I have bulk RNA-seq from a mutation sample. Would you suggest papers that only use RNA-seq but can discover novel disease mechanisms? Or papers that find target genes to treat the diseased cell that has the mutation. In my sample, a mutation in gene A caused hundreds of genes to up and down-regulate compared with control. I appreciate your help!
Hi @ialbert. Thank you for your reply! I don't asking about interpretation of my data. Just wonder if there is any related papers I can read. My question caused misunderstanding. Sorry for that!
This would be a good thing to research on your own (with PubMed/Google scholar searches).
Taking a short-cut and asking ChatGPT may also be useful. Here is what GPT produced:
Colorectal Cancer Mutations and RNA-Seq:
Paper: "Identification of a novel candidate gene, C1orf201, in a colorectal cancer GWAS linkage peak on chromosome 1p33–p34" by N. M. Cazier et al. (published in 2012 in the journal Molecular Cancer Research). Summary: This study used RNA-Seq data to explore the functional implications of a candidate gene in colorectal cancer and its potential role in the disease.
Breast Cancer Mutations and RNA-Seq:
Paper: "Mutational analysis of the tyrosine kinome in serous and clear cell endometrial cancer uncovers rare somatic mutations in TNK2 and DDR1" by M. J. O'Hara et al. (published in 2011 in the journal PLoS ONE). Summary: This research used RNA-Seq data to investigate somatic mutations in tyrosine kinases in endometrial cancer, contributing to a better understanding of the disease.
Lung Cancer Mutations and RNA-Seq:
Paper: "Comprehensive genomic profiles of small cell lung cancer" by J. R. George et al. (published in 2015 in the journal Nature). Summary: This study combined RNA-Seq and whole-genome sequencing data to explore the mutational landscape of small cell lung cancer, revealing novel mutated genes associated with the disease.
Neurological Disorders and Mutations with RNA-Seq:
Paper: "Mutations in the gene encoding capillary morphogenesis protein 2 cause juvenile hyaline fibromatosis and infantile systemic hyalinosis" by E. Sun et al. (published in 2013 in the journal American Journal of Human Genetics). Summary: This paper employed RNA-Seq and other genomic techniques to identify mutations in a specific gene associated with neurological disorders.
Thanks @genomax. Just not sure key word to use in this case, RNA-seq may not specific enough. Currently I only have RNA-seq but not GWAS.
correlation between mutated genes, disease, and RNA-Seq data without relying on Genome-Wide Association Studies (GWAS):
Thank you so much. I think you aware that many papers from chatGPT don't exist.
That is why use GPT only as a rough guide. If you have access to a tool like IPA you will get validated information but it is going to cost a pretty penny.