DATA NEWSLETTER :: 17 APR 2008

Compendia Bioscience announces the addition of 19 highly curated data sets to the Oncomine database. More than 60% of these include data not found in GEO.
⁺ include data not found in GEO
include drug treatment data

New Pathway Datasets

Cloughesy_Brain⁺	Samples: 16
Antitumor activity of rapamycin in a Phase I trial for patients with recurrent PTEN-deficient glioblastoma.	Analyses: 2
	PLoS Med 2008
	PMID: 18215105

Lapointe_Prostate_2⁺	Samples: 64
Genomic profiling reveals alternative genetic pathways of prostate tumorigenesis.	Analyses: 10
	Cancer Res 2007
	PMID: 17875689

Ferreira_Sarcoma⁺	Samples: 25
Array CGH and gene-expression profiling reveals distinct genomic instability patterns associated with DNA repair and cell-cycle checkpoint pathways in Ewing's sarcoma.	Analyses: 5
	Oncogene 2007
	PMID: 17952124

Ferreira_Sarcoma_2⁺	Samples: 14
Array CGH and gene-expression profiling reveals distinct genomic instability patterns associated with DNA repair and cell-cycle checkpoint pathways in Ewing's sarcoma.	Analyses: 5
	Oncogene 2007
	PMID: 17952124

Amit_CellLine	Samples: 7
A module of negative feedback regulators defines growth factor signaling.	Analyses: 1
	Nat Genet 2007
	PMID: 17322878

Amit_CellLine_2	Samples: 13
A module of negative feedback regulators defines growth factor signaling.	Analyses: 2
	Nat Genet 2007
	PMID: 17322878

Buess_CellLine⁺	Samples: 95
Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer.	Analyses: 2
	Genome Biol 2007
	PMID: 17868458

Dohda_CellLine	Samples: 6
Notch signaling induces SKP2 expression and promotes reduction of p27Kip1 in T-cell acute lymphoblastic leukemia cell lines.	Analyses: 1
	Exp Cell Res 2007
	PMID: 17560996

Gemma_CellLine⁺	Samples: 29
Anticancer drug clustering in lung cancer based on gene expression profiles and sensitivity database.	Analyses: 8
	BMC Cancer 2006
	PMID: 16813650

Kim_CellLine	Samples: 5
Activation of p53-dependent growth suppression in human cells by mutations in PTEN or PIK3CA.	Analyses: 1
	Mol Cell Biol 2007
	PMID: 17060456

Olejniczak_CellLine⁺	Samples: 34
Integrative genomic analysis of small-cell lung carcinoma reveals correlates of sensitivity to bcl-2 antagonists and uncovers novel chromosomal gains.	Analyses: 2
	Mol Cancer Res 2007
	PMID: 17426248

Olejniczak_CellLine_2⁺	Samples: 23
Integrative genomic analysis of small-cell lung carcinoma reveals correlates of sensitivity to bcl-2 antagonists and uncovers novel chromosomal gains.	Analyses: 1
	Mol Cancer Res 2007
	PMID: 17426248

ONeil_CellLine⁺	Samples: 18
FBW7 mutations in leukemic cells mediate NOTCH pathway activation and resistance to gamma-secretase inhibitors.	Analyses: 2
	J Exp Med 2007
	PMID: 17646409

Palomero_CellLine⁺	Samples: 20
Mutational loss of PTEN induces resistance to NOTCH1 inhibition in T-cell leukemia.	Analyses: 2
	Nat Med 2007
	PMID: 17873882

Palomero_CellLine_2⁺	Samples: 28
NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth.	Analyses: 7
	Proc Natl Acad Sci USA 2006
	PMID: 17114293

Tiwari_CellLine_2	Samples: 3
Gene expression profiling in prostate cancer cells with Akt activation reveals Fra-1 as an Akt-inducible gene.	Analyses: 1
	Mol Cancer Res 2003
	PMID: 12692267

Wagner_CellLine⁺	Samples: 119
Death-receptor O-glycosylation controls tumor-cell sensitivity to the proapoptotic ligand Apo2L/TRAIL.	Analyses: 9
	Nat Med 2007
	PMID: 17767167

Yu_CellLine	Samples: 11
Integrative genomics analysis reveals silencing of beta-adrenergic signaling by polycomb in prostate cancer.	Analyses: 2
	Cancer Cell 2007
	PMID: 17996646

Yu_CellLine_2	Samples: 12
Integrative genomics analysis reveals silencing of beta-adrenergic signaling by polycomb in prostate cancer.	Analyses: 2
	Cancer Cell 2007
	PMID: 17996646

Updated ExpO Dataset

Paired aCGH/mRNA Datasets

Paired aCGH/mRNA Datasets
aCGH Dataset Name:	mRNA Dataset Name:
Ferreira_Sarcoma	Ferreira_Sarcoma_2
Lapointe_Prostate_2	Lapointe_Prostate
Olejniczak_CellLine_2	Olejniczak_CellLine
Kotliarov_Brain	Sun_Brain
Pollack_Breast	Pollack_Breast_2

Additional Literature-Defined Concepts

Type:	Concept Name:
ChIP-on-chip	Genes with ERa binding site(s) within 20kb of transcriptional start site
	Genes with ERa binding site(s) within 60kb of transcriptional start site
	Genes with NOTCH1 binding site(s)
shRNA	shRNAs that reduce viability of DLD-1 colon cancer cells
	shRNAs that reduce viability of HCC-1954 breast cancer cells
	shRNAs that reduce viability of HCT116 colon cancer cells
	shRNAs that reduce viability of human mammary epithelial cells (HMECs)
	shRNAs that reduce viability of MDA-MB-231 breast adenocarcinoma cells
	shRNAs that reduce viability of MCF-10A non-tumorigenic breast epithelial cells
	shRNAs that reduce viability of T47D ductal breast adenocarcinoma cells
	shRNAs that reduce viability of MDA-MB-435S ductal breast adenocarcinoma cells
IGF Pathway	Down-regulated genes in IGF1-transfected MCF7 cells as compared to MCF7-vector control cells
	Up-regulated genes in IGF1-transfected MCF7 cells as compared to MCF7-vector control cells
	Up-regulated genes in IGF2-transfected MCF7 cells as compared to MCF7-vector control cells
	Up-regulated genes in human prostate cancer LNCaP cells grown as mouse xenografts on High Fat Diet as compared to Low Fat Diet
	Down-regulated genes in human prostate cancer LNCaP cells grown as mouse xenografts on High Fat Diet as compared to Low Fat Diet