Identifying common transcriptome signatures of cancer by interpreting deep learning models, Genome Biology
Por um escritor misterioso
Last updated 05 julho 2024
![Identifying common transcriptome signatures of cancer by interpreting deep learning models, Genome Biology](https://media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs13059-022-02681-3/MediaObjects/13059_2022_2681_Fig1_HTML.png)
Background Cancer is a set of diseases characterized by unchecked cell proliferation and invasion of surrounding tissues. The many genes that have been genetically associated with cancer or shown to directly contribute to oncogenesis vary widely between tumor types, but common gene signatures that relate to core cancer pathways have also been identified. It is not clear, however, whether there exist additional sets of genes or transcriptomic features that are less well known in cancer biology but that are also commonly deregulated across several cancer types. Results Here, we agnostically identify transcriptomic features that are commonly shared between cancer types using 13,461 RNA-seq samples from 19 normal tissue types and 18 solid tumor types to train three feed-forward neural networks, based either on protein-coding gene expression, lncRNA expression, or splice junction use, to distinguish between normal and tumor samples. All three models recognize transcriptome signatures that are consistent across tumors. Analysis of attribution values extracted from our models reveals that genes that are commonly altered in cancer by expression or splicing variations are under strong evolutionary and selective constraints. Importantly, we find that genes composing our cancer transcriptome signatures are not frequently affected by mutations or genomic alterations and that their functions differ widely from the genes genetically associated with cancer. Conclusions Our results highlighted that deregulation of RNA-processing genes and aberrant splicing are pervasive features on which core cancer pathways might converge across a large array of solid tumor types.
![Identifying common transcriptome signatures of cancer by interpreting deep learning models, Genome Biology](https://www.biorxiv.org/content/biorxiv/early/2021/11/12/2021.11.11.467790/F3.large.jpg)
Identifying common transcriptome signatures of cancer by
![Identifying common transcriptome signatures of cancer by interpreting deep learning models, Genome Biology](https://www.frontiersin.org/files/Articles/1285795/fmolb-10-1285795-HTML/image_m/fmolb-10-1285795-g002.jpg)
Frontiers Machine learning for pan-cancer classification based
![Identifying common transcriptome signatures of cancer by interpreting deep learning models, Genome Biology](https://www.mdpi.com/ijms/ijms-22-05751/article_deploy/html/images/ijms-22-05751-g001.png)
IJMS, Free Full-Text
![Identifying common transcriptome signatures of cancer by interpreting deep learning models, Genome Biology](https://www.frontiersin.org/files/Articles/586602/fgene-11-586602-HTML/image_m/fgene-11-586602-g001.jpg)
Frontiers Multi-Approach Bioinformatics Analysis of Curated
![Identifying common transcriptome signatures of cancer by interpreting deep learning models, Genome Biology](https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41392-022-00960-w/MediaObjects/41392_2022_960_Fig1_HTML.png)
Clinical and translational values of spatial transcriptomics
![Identifying common transcriptome signatures of cancer by interpreting deep learning models, Genome Biology](https://media.springernature.com/m685/springer-static/image/art%3A10.1038%2Fs41467-021-25534-2/MediaObjects/41467_2021_25534_Fig1_HTML.png)
Learning interpretable cellular and gene signature embeddings from
![Identifying common transcriptome signatures of cancer by interpreting deep learning models, Genome Biology](https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41568-022-00502-0/MediaObjects/41568_2022_502_Fig1_HTML.png)
Big data in basic and translational cancer research
![Identifying common transcriptome signatures of cancer by interpreting deep learning models, Genome Biology](https://www.mdpi.com/cancers/cancers-15-03237/article_deploy/html/images/cancers-15-03237-g001.png)
Cancers, Free Full-Text
![Identifying common transcriptome signatures of cancer by interpreting deep learning models, Genome Biology](https://www.researchgate.net/publication/360656074/figure/fig5/AS:11431281096995502@1668397877781/Protein-domains-that-are-affected-by-at-least-two-splice-junctions-with-high-attributions_Q320.jpg)
PDF) Identifying common transcriptome signatures of cancer by
![Identifying common transcriptome signatures of cancer by interpreting deep learning models, Genome Biology](https://www.biorxiv.org/content/biorxiv/early/2021/11/12/2021.11.11.467790/F1.large.jpg)
Identifying common transcriptome signatures of cancer by
![Identifying common transcriptome signatures of cancer by interpreting deep learning models, Genome Biology](https://media.springernature.com/m685/springer-static/image/art%3A10.1038%2Fs41597-019-0207-2/MediaObjects/41597_2019_207_Fig1_HTML.png)
Compendiums of cancer transcriptomes for machine learning
![Identifying common transcriptome signatures of cancer by interpreting deep learning models, Genome Biology](https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41467-022-32205-3/MediaObjects/41467_2022_32205_Fig1_HTML.png)
Connecting omics signatures and revealing biological mechanisms
![Identifying common transcriptome signatures of cancer by interpreting deep learning models, Genome Biology](https://www.mdpi.com/cancers/cancers-14-01185/article_deploy/html/images/cancers-14-01185-g002.png)
Cancers, Free Full-Text
![Identifying common transcriptome signatures of cancer by interpreting deep learning models, Genome Biology](https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41598-023-35842-w/MediaObjects/41598_2023_35842_Fig1_HTML.png)
Deep learning model accurately classifies metastatic tumors from
Recomendado para você
-
Test your brain power on Zoom in August! - General News - News05 julho 2024
-
Brain Test Level 367 Answer It's Cold, The Fireplace Needs More Fire, Brain Test Level 367 Walkthrough - News05 julho 2024
-
Hodological organization of spoken language production and singing in the human brain05 julho 2024
-
d-Amino Acid Levels in Perfused Mouse Brain Tissue and Blood: A Comparative Study05 julho 2024
-
Ephaptic Interactions in the Mammalian Olfactory System05 julho 2024
-
Effectiveness of management strategies for uninvestigated dyspepsia: systematic review and network meta-analysis05 julho 2024
-
Gone West: Boeing Test Pilot James Gannett05 julho 2024
-
Page 6 1,000+ Logo Alzheimers Care Pictures05 julho 2024
-
Corticostriatal circuits in the transition to chronic back pain: The predictive role of reward learning - ScienceDirect05 julho 2024
-
Trexall: Package Insert05 julho 2024
você pode gostar
-
Lowercase Russian alphabet lore Comic Studio - make comics & memes with Lowercase Russian alphabet lore characters05 julho 2024
-
Everything You Need to Know from the Genshin Impact 4.3 Livestream - KeenGamer05 julho 2024
-
roblox id catalog|TikTok Search05 julho 2024
-
Chibi Naruto Uzumaki - adorably funny anime pfp - Image Chest05 julho 2024
-
To the Theme Park!05 julho 2024
-
Modern Warfare 2 'connection failed' screen error: How to fix, possible reason, and more05 julho 2024
-
Influencer detido em operação contra rifas ilegais ostenta carros de luxo nas redes05 julho 2024
-
Terraria Boss - Root of Life by HallowAngel on DeviantArt05 julho 2024
-
Heroes of the Storm Map Tier List05 julho 2024
-
YUMMY TOAST - Jogue Grátis Online!05 julho 2024