Genomics + Informatics Applications & Datasets

	GNF Genome Informatics Applications & Datasets

Disclaimer: By using this site and any of its links, materials, documentation, applications, or datasets you acknowledge that you have read, and agree with, the Terms Of Use.

Download Data

Expression Data:
- Human U133A + GNF1H (MAS5-condensed) GeneAtlas (8.5M), also available with Affymetrix MAS5 Absent/Present calls for the HG-U133A and GNF1H probesets, respectively.
- Human U133A + GNF1H (gcRMA-condensed) GeneAtlas (7M)
- Mouse GNF1M (MAS5-condensed) GeneAtlas (9.2M), also available with Affymetrix MAS5 Absent/Present calls
- Mouse GNF1M (gcRMA-condensed) GeneAtlas (5M)
- NCI60 on U133A analyzed with MAS5, also available with A/P calls, or gcRMA-analyzed (10M)
- Ratlas, MAS5 (2M) and gcRMA-analyzed Ratlas (6M)
Chip Annotation Mouse GNF1M (1.3M, updated May 2007) or Human GNF1H (0.5M, updated May 2007)
Earlier Chip Annotation Mouse GNF1M (5.2M, updated March 2006) or Human GNF1H (0.8M)
Sample Annotation:
- Human and Mouse Body Atlas
- NCI60 Cell-Line datasets (or use table in Excel format), amplification kits
RCT (Regions of Correlated Transcription) data files for human and mouse

Quick Links

Applications: SymAtlas \| GeneAtlas v2	Search gene symbol, name, or accession:
Raw Dataset Requests: Human & Mouse Transcriptome Profiling
Terms Of Use

Publications & References

HG_U133A/GNF1H and GNF1M Tissue Atlas Datasets. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A.
Supplementary Material:
- Tissue Annotation: Human, Mouse
- Searchable Applications: SymAtlas, GeneAtlas v2
- RCT data files for human and mouse
- Annotation tables for GNF1M and GNF1H public probesets.
HG_U95A and MG_U74A Tissue Atlas Datasets. Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega RG, Sapinoso LM, Moqrich A, Patapoutian A, Hampton GM, Schultz PG, Hogenesch JB. (2002) Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A.
Supplementary Material:
- Searchable Applications: SymAtlas, GeneAtlas v1
RG_U34A Tissue Atlas Datasets. Walker JR, Su AI, Self DW, Hogenesch JB, Lapp H, Maier R, Hoyer D and Bilbe G (2004) Applications of a rat multiple tissue gene expression dataset. Genome Research.
Supplementary Material:
- Searchable Applications: SymAtlas, GeneAtlas v1
Applications and Databases. A manuscript explaining the SymGene database schema, SymAtlas application, the process flow, and the software architecture is in preparation.

External References

Affymetrix Statistical Algoritms Description white paper
MAS5: Hubbell, E., et al. Robust estimators for expression analysis. Bioinformatics. 2002, 18(12):1585-92
gcRMA: Zhijin Wu, Rafael A. Irizarry, Robert Gentleman, Francisco Martinez Murillo, and Forrest Spencer, A Model Based Background Adjustment for Oligonucleotide Expression Arrays (May 28, 2004). Johns Hopkins University, Dept. of Biostatistics Working Papers. Working Paper 1.
gcRMA: Wu, Z and Irizarry, RA, Stochastic Models Inspired by Hybridization Theory for Short Oligonucleotide Arrays. Proceedings of RECOMB 2004 (PDF). Also in J Comput Biol. 2005 Jul-Aug;12(6):882-93.

Disclaimer: By using this site and any of its links, materials, documentation, applications, or datasets you acknowledge that you have read, and agree with, the Terms Of Use.