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Datasets list

Below is the list of all publications whose data compose our gene expression compendium. For each publication, we also list the number of arrays it had and the abbreviation we gave it, where the abbreviation are used to name the expression clusters from each publication that we used as part of our collection of gene sets.

#PublicationAbbreviationArraysPlatformCategorySamplesInterpretation
1Alizadeh et al.Alizadeh00134cDNA (Stanford)B lymphomaB cell lymphomasDifferences between various types of B cell lymphomas
2Armstrong et al.Armstrong0172Hu95 (Affymetrix)LeukemiaAcute Lymphocytic Leukemia (ALL)Differences between ALL sub-types
3Bhattacharjee et al.Bhattacharjee01203Hu95 (Affymetrix)Lung cancerNormal lung and lung cancer: adenocarcinoma, squamous cell carcinoma and carcinooidDifferences between various types of lung cancer and normal lung
4Blader et al.Blader0118cDNA (Stanford)Fibroblast infectionToxoplasma infected human foreskin fibrobalstsResponse of fibroblasts to infection
5Boldrick et al.Boldrick02183cDNA (Stanford)Stimulated PBMCHuman peripheral blood mononuclear cells responding to bacteria and bacterial productsDifferences between stimulated and non-stimulated PBMCs and between various types of stimuli
6Chen et al.Chen02207cDNA (Stanford)Liver cancerHepatitis infected liver and hepatocellular carcinomaDifferences between non-tumor (mostly hepaitis) liver and HCC
7Cuadras et al.Cuadras0216cDNA (Stanford)Viral infectionRotavirus infected cellsResponse of cells to viral infection
8Detweiler et al.Detweiler0153cDNA (Stanford)Stimulated immuneHuman macrophage cell line (U937) response to SalmonellaDifferences between mock and bacterial infected cells, both PBMCs and monocytes
9Garber et al.Garber0173cDNA (Stanford)Lung cancerNormal lung and lung cancer: adenocarcinoma, squamous cell carcinoma and carcinooidDifferences between various types of lung cancer and normal lung
10Golub et al.Golub9970HuGeneFL (Affymetrix)LeukemiaAcute Lymphocytic Leukemia (ALL) and Acute Myelocytic Leukemia (AML)Differences between ALL and AML
11Iyer et al.Iyer9918cDNA (Stanford)Fibroblast serumSerum response in primary human fibroblastsTemporal response of human fibroblasts to serum
12Lessnick et al.Lessnick0210Hu95 (Affymetrix)Fibroblast EWS-FLIExtended lifespan human fibroblasts expressing the EWS/FLI oncogenTemporal response to EWS/FLI induction in fibroblasts
13Nutt et al.Nutt0347Hu95 (Affymetrix)GliomasMalignant gliomasDifferences between various gliomas
14Perou et al.Perou0084cDNA (Stanford)Breast cancerNormal breast, breast cancer, human mammary epithelial cells and breast cancer cell linesDifferences between breast tissue, cancer, cells and cell lines
15Perou et al.Perou9926cDNA (Stanford)Breast cancerNormal breast, breast cancer, human mammary epithelial cells and breast cancer cell linesDifferences between breast tissue, cancer, cells and cell lines
16Pollack et al.Pollack9910cDNA (Stanford)
17Pomeroy et al.Pomeroy0290HuGeneFL (Affymetrix)Neuro tumorsCentral nervous system. Embryonal tumours: medulloblastomas, primitive neuroectodermal tumors (PNETs), atypical teratoid/rhabdoid tumors, and malignant gliomasDifferences between different neurological tumors, mostly embryonal
18Ramaswamy et al.Ramaswamy01155HuGeneFL (Affymetrix)Various tumorsLarge variety of tumors and normal tissuesDifferences between various tumors and normal tissues
19Rosenwald et al.Rosenwald01102cDNA (Stanford)B lymphomaB cell lymphomasDifferences between various B lymphomas
20Ross et al.Ross0068cDNA (Stanford)NCI60NCI cell linesDifferences between the various NCI cell lines
21Ross et al.Ross0124cDNA (Stanford)NCI60NCI cell linesDifferences between the various NCI cell lines
22Shipp et al.Shipp0277HuGeneFL (Affymetrix)B lymphomaB cell lymphomasDifferences between various B lymphomas
23Singh et al.Singh02102Hu95 (Affymetrix)Prostate cancerNormal prostate and prostate cancerDifferences between prostate cancer and normal prostate
24Sorlie et al.Sorlie0185cDNA (Stanford)Breast cancerNormal breast and breast cancerDifferences between different breast carcinomas
25Stuanton et al.Staunton0160HuGeneFL (Affymetrix)NCI60NCI cell linesDifferences between the various NCI cell lines
26Whitfield et al.Whitfield02114cDNA (Stanford)HeLa cell cycleHeLa Cell cycleDifferences between the various stages of the HeLa cell cycle