A DNA microarray survey of gene expression in normal human tissues

doi:10.1186/gb-2005-6-3-r22

Genome Biology

Volume 6
Issue 3

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Shyamsundar R
Kim YH
Higgins JP
Montgomery K
Jorden M
Sethuraman A
van de Rijn M
Botstein D
Brown PO
Pollack JR

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Kim YH
Higgins JP
Montgomery K
Jorden M
Sethuraman A
van de Rijn M
Botstein D
Brown PO
Pollack JR
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A correction for this article has been published in Genome Biology 2005, 6:404

Research

A DNA microarray survey of gene expression in normal human tissues

Radha Shyamsundar¹^,2 , Young H Kim¹ , John P Higgins¹ , Kelli Montgomery¹ , Michelle Jorden¹ , Anand Sethuraman³ , Matt van de Rijn¹ , David Botstein³^,5 , Patrick O Brown²^,4 and Jonathan R Pollack¹

¹Department of Pathology, Stanford University School of Medicine, 269 Campus Drive, CCSR 3245A, Stanford, CA 94305-5176, USA

²Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305-5307, USA

³Department of Genetics, Stanford University, Stanford, CA 94305, USA

⁴Howard Hughes Medical Institute, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305-5307, USA

⁵Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 80544, USA

author email corresponding author email

Genome Biology 2005, 6:R22doi:10.1186/gb-2005-6-3-r22


Published:	14 February 2005

Subject areas: Genome studies, Methods, Medicine, Cancer

Additional files

Additional File 1:

A table listing the normal tissue specimens included in microarray analysis

Format: TXT Size: 3KB Download file

Additional File 2:

A table listing the variably expressed genes. Sheet 1: Dataset represented in Fig. 1, which includes well-measured genes in ≥ 75% of samples, and with ≥ 4-fold ratio variation from the mean in at least 2 samples; samples ordered by clustering.Sheet 2: Variably expressed genes which are well-measured in ≥ 75% of samples, with ≥ 2-fold ratio variation from the mean in at least 2 samples; samples ordered by anatomic site. Sheet 3: Variably expressed genes which are well-measured in ≥ 25% of samples, with ≥ 4-fold ratio variation from the mean in at least 2 samples; samples ordered by anatomic site. Sheet 4: Same dataset as sheet 1, but here ratios represent relative transcript abundance (See Materials and methods). Sheet 5: Same dataset as sheet 2, but here ratios represent relative transcript abundance (See Materials and methods). Sheet 6: Same dataset as sheet 3, but here ratios represent relative transcript abundance (See Materials and methods)

Format: ZIP Size: 27.5MB Download file

Additional File 3:

A table listing tissue-specific transcripts

Format: XLS Size: 8.5MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 4:

A table listing functionally annotated gene sets

Format: XLS Size: 3.7MB Download file

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Additional File 5:

A table listing highly abundant tissue-specific transcripts

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Additional File 6:

A figure showing tissue-specific gene expression. Variably-expressed genes determined to be expressed in a tissue-selective fashion using the SAM method are depicted as described in the legend to manuscript Figure 2. a, brain; b, salivary gland; c, esophagus; d, stomach; e, small bowel; f, colon; g, pancreas; h, liver; i, heart; j, skeletal muscle; k, lung; l, kidney; m, bladder;n, prostate; o, seminal vesicle; p, testis; q, ovary; r, fallopian tube; s, uterus; t, cervix, u, thyroid; v, parathyroid; w, adrenal; x, lymph node; y, tonsil; z, thymus; aa, spleen; bb, buffy coat

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Additional File 7:

A figure showing expression of functionally annotated gene sets. Hierarchical cluster of 115 normal tissue specimens and annotated gene sets representing examples of specific molecular functions, cellular components, or biological processes. a, tyrosine kinase (activity); b, kinase (activity); c, G-protein coupled receptor (activity); d, transcription factor activity; e, ion channel (activity); f, extracellular matrix (component), g, cell adhesion (process); h, programmed cell death (process)

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Additional File 8:

A figure showing highly abundant tissue-specific gene expression. Highly-abundant tissue specific transcripts were defined for each tissue type as the top (capped at 50 genes) tissue specific transcripts, identified using the SAM method, from the 1000 most abundantly expressed transcripts in the full dataset. a, brain; b, salivary gland; c, esophagus; d, stomach; e, small bowel; f, colon; g, pancreas; h, liver; i, heart; j, skeletal muscle; k, lung; l, kidney; m, bladder;n, prostate; o, seminal vesicle; p, testis; q, ovary; r, fallopian tube; s, uterus; t, cervix, u, thyroid; v, parathyroid; w, adrenal; x, lymph node; y, tonsil; z, thymus; aa, spleen; bb, buffy coat

Format: PDF Size: 1.1MB Download file

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