Novel disease mechanism papers from RNA-seq

Question

[Chris]

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!

Answer 1

[Istvan Albert]

if you are asking about interpretation of your data - we can't help with that.

the analysis provides supporting evidence for certain changes in the transcriptome - but it is the domain expert that has to put those changes into the proper context

[Chris]

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!

[GenoMax]

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:

1. 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.

2. 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.

3. 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.

4. 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.

[Chris]

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.

[GenoMax]

correlation between mutated genes, disease, and RNA-Seq data without relying on Genome-Wide Association Studies (GWAS):

     1. Pancreatic Cancer and RNA-Seq:
        Paper: "Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma" by The Cancer Genome Atlas Research Network (published in 2017 in the journal Cancer Cell).
        Summary: This study used RNA-Seq data to identify mutated genes and pathways associated with pancreatic ductal adenocarcinoma.

   2.  Leukemia Mutations and RNA-Seq:
        Paper: "Genomic analysis of chronic lymphocytic leukemia subtypes" by C. Landau et al. (published in 2013 in the journal Cell).
        Summary: This research employed RNA-Seq to investigate the genomic landscape of chronic lymphocytic leukemia, including mutated genes and their functional implications.

    3. Lung Cancer Mutations and RNA-Seq:
        Paper: "Comprehensive Molecular Profiling of Lung Adenocarcinoma" by R. Govindan et al. (published in 2012 in the journal Nature).
        Summary: This study used RNA-Seq and other genomic techniques to identify mutated genes in lung adenocarcinoma and understand their roles in the disease.

    4. Breast Cancer Mutations and RNA-Seq:
        Paper: "Characterization of the Genomic Landscape of Breast Cancer through Massively Parallel Sequencing" by M. S. Ellis et al. (published in 2012 in the journal Genome Research).
        Summary: This paper combined RNA-Seq and whole-genome sequencing to identify mutations in breast cancer and explore their functional consequences.

    5. Glioblastoma Mutations and RNA-Seq:
        Paper: "Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas" by The Cancer Genome Atlas Research Network (published in 2015 in the journal New England Journal of Medicine).
        Summary: This study utilized RNA-Seq data to investigate the genomics of lower-grade gliomas, including mutated genes and their relevance to the disease.

[Chris]

Thank you so much. I think you aware that many papers from chatGPT don't exist.

[GenoMax]

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.