Datasets on BioGPS
Looking for the datasets used in BioGPS? We've made them easily available for download right here.
| GEO code | CSV download | Sample Annotation | |
|---|---|---|---|
| Human U133A/GNF1H Gene Atlas | GSE1133 | gnf1h-gcrma.zip averaged (4.1 MB) gnf1h-gcrma-unaveraged.zip (7.1 MB) | human_sample_annot.csv (12 KB) |
| Human NCI60 Cell Lines | N/A CEL files | NCI60_U133A_20070815.raw.csv.zip (6.2 MB) | NCI60_sample_info.xls (92 KB) |
| Mouse GNF1M Gene Atlas | GSE1133 | GNF1M_geneatlas_20120817.zip (4.9 MB) | N/A |
| Mouse MOE430 Gene Atlas | GSE10246 | geneatlas_MOE430_20090327.raw.avg.csv.zip averaged (12.7 MB) geneatlas_MOE430_20090327.raw.csv.zip (17 MB) | N/A |
| Rat RGU34A Gene Atlas | GSE952 | Ratlas-gcRMA.zip (5.9 MB) | N/A |
| Human Primary Tumors (U95) | N/A | primary_tumor_classification_data.txt.zip (4.1 MB) | primary_tumor_sample_annot.zip (24 KB) |
| Mouse Exon Array Gene Atlas | GSE15998 | N/A | N/A |
| Mouse Adipose eQTL | N/A | adipose_MOE430_20071005.raw.csv.gz (3.4 MB) | N/A |
Chip Annotation
| Chip Name | Chip Annotation File | Updated | GEO Platform Accession |
|---|---|---|---|
| Mouse GNF1M | gnf1m-anntable.zip (1.3 MB) | May 2007 | GPL1073 |
| Human GNF1H | gnf1h-anntable.zip (0.5 MB) | May 2007 | GPL1074 |
| Human U133A | Maintained by Affymetrix | GPL96 | |
| Mouse MOE430 2.0 | Maintained by Affymetrix | GPL1261 | |
Publications & References
| Subject | Citation | PubMed | |
|---|---|---|---|
| BioGPS Application | Wu C, Jin X, Tsueng G, Afrasiabi C, and Su AI (2016) BioGPS: building your own mash-up of gene annotations and expression profiles. Nucl. Acids Res. 44(D1): D313-D316. (*Database Issue*)
Wu C, MacLeod I, Su AI (2013) BioGPS and MyGene.info: organizing online, gene-entric information. Nucl. Acids Res. 41(D1): D561-D565. (*Database Issue*) Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW 3rd, Su AI (2009) BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol. 10(11):R130. |  |  |
| Circadian genomics screen | Zhang EE, Liu AC, Hirota T, Miraglia LJ, Welch G, Pongsawakul PY, Liu X, Atwood A, Huss JW 3rd, Janes J, Su AI, Hogenesch JB, Kay SA. (2009) A genome-wide RNAi screen for modifiers of the circadian clock in human cells. Cell. 139(1):199-210. | | |
| MOE430 Gene Atlas Data set | Lattin JE, Schroder K, Su AI, Walker JR, Zhang J, Wiltshire T, Saijo K, Glass CK, Hume DA, Kellie S, Sweet MJ (2008) Expression analysis of G Protein-Coupled Receptors in mouse macrophages. Immunome Res. 4:5. | | |
| eQTL Adipose Data set | Wu C, Delano DL, Mitro N, Su SV, Janes J, McClurg P, Batalov S, Welch GL, Zhang J, Orth AP, Walker JR, Glynne RJ, Cooke MP, Takahashi JS, Shimomura K, Kohsaka A, Bass J, Saez E, Wiltshire T, Su AI (2008) Gene set enrichment in eQTL data identifies novel annotations and pathway regulators. PLoS Genetics 4(5):e1000070. | | |
| eQTL Hypothalamus Data set | McClurg P, Janes J, Wu C, Delano DL, Walker JR, Batalov S, Takahashi JS, Shimomura K, Kohsaka A, Bass J, Wiltshire T, Su AI (2007) Genomewide association analysis in diverse inbred mice: power and population structure. Genetics 176(1):675-83. | | |
| HG_U133A/GNF1H and GNF1M Gene Atlas Data sets | 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. 101(16):6062-7. | | |
| HG_U95A and MG_U74A Gene Atlas Data sets | 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. 99(7):4465-70. | | |
| RG_U34A Gene Atlas Data set | 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 Res. 14(4):742-9. | | |
| Primary Tumors (U95) Data set | Su AI, Welsh JB, Sapinoso LM, Kern SG, Dimitrov P, Lapp H, Schultz PG, Powell SM, Moskaluk CA, Frierson HF Jr, Hampton GM (2001) Molecular classification of human carcinomas by use of gene expression signatures. Cancer Res. 61(20):7388-93. | | |
Graphics, Logos, etc.
Want to link to BioGPS? Writing an article or giving a presentation? We've put together a collection of graphics for you to use. Simply right-click on any of the images below and save it.
If the images here aren't quite what you need, feel free to contact us and we can help.
| Image | File Type | Background | Dimensions | Size |
|---|---|---|---|---|
 | PNG | Transparent | 618 x 190 | 49 KB |
 | PNG | Transparent | 280 x 82 | 20 KB |
 | PNG | Transparent | 100 x 143 | 23 KB |