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Related Concept Videos

Cell Specific Gene Expression01:58

Cell Specific Gene Expression

Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
General Transcription Factors01:30

General Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
Transcription Factors02:16

Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
Cellular Differentiation00:57

Cellular Differentiation

How does a complex organism such as a human develop from a single cell? It all starts from a single fertilized egg which gives rise to a vast array of cell types, such as nerve cells, muscle cells, and epithelial cells that characterize the adult? Throughout development and adulthood, cellular differentiation leads cells to assume their final morphology and physiology. Differentiation is the process by which unspecialized cells become specialized to carry out distinct functions.
A zygote is a...
Structure of a Gene01:30

Structure of a Gene

A gene is the fundamental unit of heredity. Every individual has two copies of each gene, one inherited from each parent. Although most people contain the same genes, there is a small fraction that is slightly different amongst people. A gene with a small difference in its sequence of DNA bases forms different alleles, contributing to different phenotypes.
However, only 1% of the DNA is composed of genes that encode proteins; the rest, 99% is non-coding DNA. This non-coding DNA performs...

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Related Experiment Video

Updated: Jun 15, 2026

Cell Type-specific Gene Expression Profiling in the Mouse Liver
10:06

Cell Type-specific Gene Expression Profiling in the Mouse Liver

Published on: September 17, 2019

Cell type-specific gene expression differences in complex tissues.

Shai S Shen-Orr1, Robert Tibshirani, Purvesh Khatri

  • 1Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA.

Nature Methods
|March 9, 2010
PubMed
Summary
This summary is machine-generated.

We developed cell type-specific significance analysis of microarrays (csSAM) to find gene expression differences in specific cell types. This method identified hundreds of previously undetectable genes in kidney transplant patients.

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Last Updated: Jun 15, 2026

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Area of Science:

  • Genomics
  • Bioinformatics
  • Immunology

Background:

  • Microarray analysis often struggles to identify cell type-specific gene expression.
  • Differential gene expression analysis is crucial for understanding biological states, such as transplant rejection.

Purpose of the Study:

  • To introduce and validate cell type-specific significance analysis of microarrays (csSAM).
  • To apply csSAM for identifying novel differentially expressed genes in post-transplant kidney recipients.

Main Methods:

  • csSAM was developed to analyze differential gene expression using microarray data and cell-type frequencies.
  • The csSAM method was validated using predesigned mixtures.
  • csSAM was applied to whole-blood gene expression datasets from kidney transplant recipients.

Main Results:

  • csSAM successfully identified cell type-specific differential gene expression.
  • Application to transplant data revealed hundreds of differentially expressed genes.
  • These genes were previously undetectable using standard methods.

Conclusions:

  • csSAM is an effective tool for cell type-specific gene expression analysis.
  • The method enhances the discovery of biomarkers in complex biological samples.
  • This approach offers new insights into the molecular mechanisms of transplant rejection.