Large-scale Analysis of the Human and Mouse Transcriptomes

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2002 Mar 21

PMID 11904358

Citations 684

Authors

Andrew I Su

Michael P Cooke

Keith A Ching

Yaron Hakak

John R Walker

Tim Wiltshire

Anthony P Orth

Raquel G Vega

Lisa M Sapinoso

Aziz Moqrich

Ardem Patapoutian

Garret M Hampton

Peter G Schultz

John B Hogenesch

Affiliations

Soon will be listed here.

Abstract

High-throughput gene expression profiling has become an important tool for investigating transcriptional activity in a variety of biological samples. To date, the vast majority of these experiments have focused on specific biological processes and perturbations. Here, we have generated and analyzed gene expression from a set of samples spanning a broad range of biological conditions. Specifically, we profiled gene expression from 91 human and mouse samples across a diverse array of tissues, organs, and cell lines. Because these samples predominantly come from the normal physiological state in the human and mouse, this dataset represents a preliminary, but substantial, description of the normal mammalian transcriptome. We have used this dataset to illustrate methods of mining these data, and to reveal insights into molecular and physiological gene function, mechanisms of transcriptional regulation, disease etiology, and comparative genomics. Finally, to allow the scientific community to use this resource, we have built a free and publicly accessible website (http://expression.gnf.org) that integrates data visualization and curation of current gene annotations.

Citing Articles

Sundararajan R, Hegde S, Panda A, Christie J, Gadewal N, Venkatraman P Commun Biol. 2025; 8(1):55.

PMID: 39814910 PMC: 11735796. DOI: 10.1038/s42003-024-07432-7.

The androgen clock is an epigenetic predictor of long-term male hormone exposure.

Sugrue V, Prescott M, Glendining K, Bond D, Horvath S, Anderson G Proc Natl Acad Sci U S A. 2025; 122(3):e2420087121.

PMID: 39805019 PMC: 11760496. DOI: 10.1073/pnas.2420087121.

Transcriptomic Characterization of Male Formosan Pangolin () Reproductive Tract and Evaluation of Domestic Cat () as a Potential Model Species.

Mear L, Tseng I, Lin K, Hsu C, Chen S, Tsai P Animals (Basel). 2024; 14(17).

PMID: 39272377 PMC: 11394312. DOI: 10.3390/ani14172592.

Synthesis at the Interface of Chemistry and Biology.

Schultz P Acc Chem Res. 2024; 57(18):2631-2642.

PMID: 39198974 PMC: 11443489. DOI: 10.1021/acs.accounts.4c00320.

MAGEL2 (patho-)physiology and Schaaf-Yang syndrome.

Schubert T, Schaaf C Dev Med Child Neurol. 2024; 67(1):35-48.

PMID: 38950199 PMC: 11625468. DOI: 10.1111/dmcn.16018.

References

Hughes J, Estep P, Tavazoie S, Church G . Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol. 2000; 296(5):1205-14. DOI: 10.1006/jmbi.2000.3519. View

Lin B, Ferguson C, White J, Wang S, Vessella R, True L . Prostate-localized and androgen-regulated expression of the membrane-bound serine protease TMPRSS2. Cancer Res. 1999; 59(17):4180-4. View

Sandberg R, Yasuda R, Pankratz D, Carter T, Del Rio J, Wodicka L . Regional and strain-specific gene expression mapping in the adult mouse brain. Proc Natl Acad Sci U S A. 2000; 97(20):11038-43. PMC: 27144. DOI: 10.1073/pnas.97.20.11038. View

Warrington J, Nair A, Mahadevappa M, Tsyganskaya M . Comparison of human adult and fetal expression and identification of 535 housekeeping/maintenance genes. Physiol Genomics. 2000; 2(3):143-7. DOI: 10.1152/physiolgenomics.2000.2.3.143. View

Rosenfeld M, Briata P, Dasen J, Gleiberman A, Kioussi C, Lin C . Multistep signaling and transcriptional requirements for pituitary organogenesis in vivo. Recent Prog Horm Res. 2000; 55:1-13; discussion 13-4. View

Penn S, Rank D, Hanzel D, Barker D . Mining the human genome using microarrays of open reading frames. Nat Genet. 2000; 26(3):315-8. DOI: 10.1038/81613. View

Eklund L, Muona A, Lietard J, Pihlajaniemi T . Structure of the mouse type XV collagen gene, Col15a1, comparison with the human COL15A1 gene and functional analysis of the promoters of both genes. Matrix Biol. 2000; 19(6):489-500. DOI: 10.1016/s0945-053x(00)00090-1. View

Scully K, Jacobson E, Jepsen K, Lunyak V, Viadiu H, Carriere C . Allosteric effects of Pit-1 DNA sites on long-term repression in cell type specification. Science. 2000; 290(5494):1127-31. DOI: 10.1126/science.290.5494.1127. View

Harmer S, Hogenesch J, Straume M, Chang H, Han B, Zhu T . Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science. 2000; 290(5499):2110-3. DOI: 10.1126/science.290.5499.2110. View

10.

Mauro M, Druker B . Chronic myelogenous leukemia. Curr Opin Oncol. 2001; 13(1):3-7. DOI: 10.1097/00001622-200101000-00002. View

11.

Eklund L, Piuhola J, Komulainen J, Sormunen R, Ongvarrasopone C, Fassler R . Lack of type XV collagen causes a skeletal myopathy and cardiovascular defects in mice. Proc Natl Acad Sci U S A. 2001; 98(3):1194-9. PMC: 14731. DOI: 10.1073/pnas.98.3.1194. View

12.

Venter J, Adams M, Myers E, Li P, Mural R, Sutton G . The sequence of the human genome. Science. 2001; 291(5507):1304-51. DOI: 10.1126/science.1058040. View

13.

Miki R, Kadota K, Bono H, Mizuno Y, Tomaru Y, Carninci P . Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays. Proc Natl Acad Sci U S A. 2001; 98(5):2199-204. PMC: 30115. DOI: 10.1073/pnas.041605498. View

14.

Lander E, Linton L, Birren B, Nusbaum C, Zody M, Baldwin J . Initial sequencing and analysis of the human genome. Nature. 2001; 409(6822):860-921. DOI: 10.1038/35057062. View

15.

Welsh J, Sapinoso L, Su A, Kern S, Wang-Rodriguez J, Moskaluk C . Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer. Cancer Res. 2001; 61(16):5974-8. View

16.

BURKS C, Fickett J, GOAD W, Kanehisa M, Lewitter F, Rindone W . The GenBank nucleic acid sequence database. Comput Appl Biosci. 1985; 1(4):225-33. View

17.

Altschul S, Gish W, Miller W, Myers E, Lipman D . Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10. DOI: 10.1016/S0022-2836(05)80360-2. View

18.

Eddy S, Mitchison G, Durbin R . Maximum discrimination hidden Markov models of sequence consensus. J Comput Biol. 1995; 2(1):9-23. DOI: 10.1089/cmb.1995.2.9. View

19.

Sallese M, Mariggio S, Collodel G, Moretti E, Piomboni P, Baccetti B . G protein-coupled receptor kinase GRK4. Molecular analysis of the four isoforms and ultrastructural localization in spermatozoa and germinal cells. J Biol Chem. 1997; 272(15):10188-95. DOI: 10.1074/jbc.272.15.10188. View

20.

Sonnhammer E, Eddy S, Durbin R . Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins. 1997; 28(3):405-20. DOI: 10.1002/(sici)1097-0134(199707)28:3<405::aid-prot10>3.0.co;2-l. View