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Literature DB >> 17570842

Celsius: a community resource for Affymetrix microarray data.

Allen Day¹, Marc R J Carlson, Jun Dong, Brian D O'Connor, Stanley F Nelson.

Abstract

Celsius is a data warehousing system to aggregate Affymetrix CEL files and associated metadata. It provides mechanisms for importing, storing, querying, and exporting large volumes of primary and pre-processed microarray data. Celsius contains ten billion assay measurements and affiliated metadata. It is the largest publicly available source of Affymetrix microarray data, and through sheer volume it allows a sophisticated, broad view of transcription that has not previously been possible.

Entities: Chemical Disease Gene Species

Mesh：

Year: 2007 PMID： 17570842 PMCID： PMC2394754 DOI： 10.1186/gb-2007-8-6-r112

Source DB: PubMed Journal: Genome Biol ISSN： 1474-7596 Impact factor: 13.583

34 in total

1. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Authors: A Brazma; P Hingamp; J Quackenbush; G Sherlock; P Spellman; C Stoeckert; J Aach; W Ansorge; C A Ball; H C Causton; T Gaasterland; P Glenisson; F C Holstege; I F Kim; V Markowitz; J C Matese; H Parkinson; A Robinson; U Sarkans; S Schulze-Kremer; J Stewart; R Taylor; J Vilo; M Vingron
Journal: Nat Genet Date: 2001-12 Impact factor: 38.330

2. Hierarchical organization of modularity in metabolic networks.

Authors: E Ravasz; A L Somera; D A Mongru; Z N Oltvai; A L Barabási
Journal: Science Date: 2002-08-30 Impact factor: 47.728

3. The ArrayExpress gene expression database: a software engineering and implementation perspective.

Authors: Ugis Sarkans; Helen Parkinson; Gonzalo Garcia Lara; Ahmet Oezcimen; Anjan Sharma; Niran Abeygunawardena; Sergio Contrino; Ele Holloway; Philippe Rocca-Serra; Gaurab Mukherjee; Mohammadreza Shojatalab; Misha Kapushesky; Susanna-Assunta Sansone; Anna Farne; Tim Rayner; Alvis Brazma
Journal: Bioinformatics Date: 2004-11-25 Impact factor: 6.937

4. Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids.

Authors: Peter S Gargalovic; Minori Imura; Bin Zhang; Nima M Gharavi; Michael J Clark; Joanne Pagnon; Wen-Pin Yang; Aiqing He; Amy Truong; Shilpa Patel; Stanley F Nelson; Steve Horvath; Judith A Berliner; Todd G Kirchgessner; Aldons J Lusis
Journal: Proc Natl Acad Sci U S A Date: 2006-08-15 Impact factor: 11.205

5. Identifying biological themes within lists of genes with EASE.

Authors: Douglas A Hosack; Glynn Dennis; Brad T Sherman; H Clifford Lane; Richard A Lempicki
Journal: Genome Biol Date: 2003-09-11 Impact factor: 13.583

6. Cluster analysis and display of genome-wide expression patterns.

Authors: M B Eisen; P T Spellman; P O Brown; D Botstein
Journal: Proc Natl Acad Sci U S A Date: 1998-12-08 Impact factor: 11.205

7. A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database.

Authors: Simon Katz; Rafael A Irizarry; Xue Lin; Mark Tripputi; Mark W Porter
Journal: BMC Bioinformatics Date: 2006-10-23 Impact factor: 3.169

8. An ontology for cell types.

Authors: Jonathan Bard; Seung Y Rhee; Michael Ashburner
Journal: Genome Biol Date: 2005-01-14 Impact factor: 13.583

9. The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data.

Authors: Terry F Hayamizu; Mary Mangan; John P Corradi; James A Kadin; Martin Ringwald
Journal: Genome Biol Date: 2005-02-15 Impact factor: 13.583

10. Design and implementation of microarray gene expression markup language (MAGE-ML).

Authors: Paul T Spellman; Michael Miller; Jason Stewart; Charles Troup; Ugis Sarkans; Steve Chervitz; Derek Bernhart; Gavin Sherlock; Catherine Ball; Marc Lepage; Marcin Swiatek; W L Marks; Jason Goncalves; Scott Markel; Daniel Iordan; Mohammadreza Shojatalab; Angel Pizarro; Joe White; Robert Hubley; Eric Deutsch; Martin Senger; Bruce J Aronow; Alan Robinson; Doug Bassett; Christian J Stoeckert; Alvis Brazma
Journal: Genome Biol Date: 2002-08-23 Impact factor: 13.583

40 in total

1. Fibrochondrogenesis results from mutations in the COL11A1 type XI collagen gene.

Authors: Stuart W Tompson; Carlos A Bacino; Nicole P Safina; Michael B Bober; Virginia K Proud; Tara Funari; Michael F Wangler; Lisette Nevarez; Leena Ala-Kokko; William R Wilcox; David R Eyre; Deborah Krakow; Daniel H Cohn
Journal: Am J Hum Genet Date: 2010-10-28 Impact factor: 11.025

2. Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways.

Authors: Jeremy A Miller; Steve Horvath; Daniel H Geschwind
Journal: Proc Natl Acad Sci U S A Date: 2010-06-25 Impact factor: 11.205

3. Identification of mutations in TRAPPC9, which encodes the NIK- and IKK-beta-binding protein, in nonsyndromic autosomal-recessive mental retardation.

Authors: Asif Mir; Liana Kaufman; Abdul Noor; Mahdi M Motazacker; Talal Jamil; Matloob Azam; Kimia Kahrizi; Muhammad Arshad Rafiq; Rosanna Weksberg; Tanveer Nasr; Farooq Naeem; Andreas Tzschach; Andreas W Kuss; Gisele E Ishak; Dan Doherty; H Hilger Ropers; A James Barkovich; Hossein Najmabadi; Muhammad Ayub; John B Vincent
Journal: Am J Hum Genet Date: 2009-12 Impact factor: 11.025

Celsius: a community resource for Affymetrix microarray data.

1. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

2. Hierarchical organization of modularity in metabolic networks.

3. The ArrayExpress gene expression database: a software engineering and implementation perspective.

4. Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids.

5. Identifying biological themes within lists of genes with EASE.

6. Cluster analysis and display of genome-wide expression patterns.

7. A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database.

8. An ontology for cell types.

9. The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data.

10. Design and implementation of microarray gene expression markup language (MAGE-ML).

1. Fibrochondrogenesis results from mutations in the COL11A1 type XI collagen gene.

2. Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways.

3. Identification of mutations in TRAPPC9, which encodes the NIK- and IKK-beta-binding protein, in nonsyndromic autosomal-recessive mental retardation.

4. Genomic landscape of meningiomas.

5. The organization of the transcriptional network in specific neuronal classes.

6. A quick guide to large-scale genomic data mining.

7. Construction and use of gene expression covariation matrix.

8. Disease gene characterization through large-scale co-expression analysis.

9. Boolean implication networks derived from large scale, whole genome microarray datasets.

10. Conserved expression patterns predict microRNA targets.