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Related Concept Videos

Cancer-Critical Genes I: Proto-oncogenes01:33

Cancer-Critical Genes I: Proto-oncogenes

Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
Cancer-Critical Genes I: Proto-oncogenes01:33

Cancer-Critical Genes I: Proto-oncogenes

Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
Cancer-Critical Genes II: Tumor Suppressor Genes01:05

Cancer-Critical Genes II: Tumor Suppressor Genes

Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
Cancer-Critical Genes II: Tumor Suppressor Genes01:05

Cancer-Critical Genes II: Tumor Suppressor Genes

Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...

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Updated: May 19, 2026

Cancer-Associated Fibroblasts from Mouse Mammary Tumors as Tools for Molecular and Computational Studies
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Published on: July 3, 2025

Solid Tumors Pan Cancer Transcriptome: Tissue/Cancer specific expression groups at the Isoform-Level.

Pallavi Surana1, Matthew Obusan1, Ramana V Davuluri1

  • 1Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY 11794, USA.

Biorxiv : the Preprint Server for Biology
|May 18, 2026
PubMed
Summary
This summary is machine-generated.

The Solid Tumors Pan-Cancer Transcriptome (STPCaT) reveals a collapse of normal tissue-specific gene expression in cancer, identifying new cancer-testis antigens and isoform signatures for precise tumor stratification.

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Last Updated: May 19, 2026

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Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
13:24

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Published on: April 11, 2016

Area of Science:

  • Genomics and Transcriptomics
  • Cancer Biology
  • Bioinformatics

Background:

  • The human genome transcribes into diverse isoforms, with tissue-specific expression often disrupted in cancer.
  • Isoform-level dysregulation in solid tumors remains poorly understood, limiting diagnostic and therapeutic applications.
  • Existing cancer-testis antigen (CTA) databases are incomplete, missing many potential tumor biomarkers.

Purpose of the Study:

  • To systematically classify transcript expression across solid tumors and normal tissues using an isoform-centric approach.
  • To identify novel diagnostic biomarkers and unannotated CTAs through pan-cancer transcriptome analysis.
  • To develop accurate isoform signatures for stratifying glioma subtypes and enabling precision oncology.

Main Methods:

  • Development and application of STPCaT (Solid Tumors Pan-Cancer Transcriptome) analysis, extending TransTEx.
  • Classification of transcript expression across TCGA solid tumors and GTEx normal tissues.
  • Consensus clustering and random-forest feature selection for identifying discriminative isoform signatures in pan-gliomas.

Main Results:

  • STPCaT revealed a collapse of normal tissue-specific expression programs in cancer, with two dominant isoform groups: cancer-high and normal-high.
  • A significant repertoire of previously unannotated CTAs was discovered, many relevant across multiple cancers, including gliomas.
  • Highly accurate (97-98%) isoform signatures for stratifying low-grade gliomas and glioblastomas were identified using as few as five transcripts.

Conclusions:

  • STPCaT provides a scalable, isoform-resolved resource for advancing tumor stratification and biomarker discovery in solid tumors.
  • The identified isoform signatures offer potential for precision oncology applications, particularly in glioma subtyping.
  • The study highlights the critical role of isoform-level analysis in understanding cancer biology and uncovering novel therapeutic targets.