Facilitating Data Deposition

The FGED Society mission includes facilitating deposition of functional genomics datasets (e.g. microarray studies) in public archives. In addition to addressing what and how data gets deposited, we are very much concerned with seeing that authors adhere to journal requirements for data deposition. Unfortunately, the requirement for data deposition is not being sufficiently met and important datasets are not accessible (see for example Ochsner et al. (2008) Nature Methods).

Therefore, we ask that investigators seeking microarray and high-throughput sequencing-based functional genomics datasets from studies published in journals requiring deposition contact us if they are unable to get them. We will then contact the authors on your behalf and inform the journal where the study was published. We will document the results on the FGED web site to assist others seeking the same dataset and to aid reviewers of related publications and grants.

We hope that you will help us in our mission.

Recommended Data Deposition Policy

The following text is provided to journals for formulating data deposition policy:

Authors submitting manuscripts describing microarray data are required to deposit the data in compliance with MIAME with one of the following public repositories: Array Express, or GEO and to have the accession numbers available to be published in the article.

Deposition of high-throughput sequencing data for RNA (RNA-Seq) and chromatin immunoprecipitation (ChIP-Seq) with ArrayExpress or GEO in compliance with MINSEQE is also required.

Submission information:
ArrayExpress: www.ebi.ac.uk/microarray/submissions_overview.html
GEO: www.ncbi.nlm.nih.gov/geo/info/submission.html

Missing Data Reports

Citation	Authors	When the request was submitted	Any response from journal or authors
Use of Gene Expression Profiles of Peripheral Blood Lymphocytes to Distinguish BRCA1 Mutation Carriers in High Risk Breast Cancer Families. Cancer Inform 2009, 7:41-56.	Vuillaume ML, Uhrhammer N, Vidal V, Vidal VS, Chabaud V, Jesson B, Kwiatkowski F, Bignon YJ	13 Oct 2009	Corresponding author was emailed Oct. 16, 2009 - no response. Publisher and Editorial Board members were contacted Oct. 29, 2009 - discussion started Nov. 19, 2009 about policy. Policy requiring microarray deposition posted Jan. 22, 2010.
Gene expression analysis in a canine model of X-linked Alport syndrome. Mamm Genome. 2006 Sep;17(9):976-90. (Pubmed ID 16964446)	Greer KA, Higgins MA, Cox ML, Ryan TP, Berridge BR, Kashtan CE, Lees GE, Murphy KE.	15 Jan 2010	Corresponding author was emailed Jan. 20, 2010 - no response. Journal was contacted March 1, 2010. Managing editor responded March 9, 2010 requesting wording for policy.Recommended policy wording was approved March 19, 2010 and is now posted.
Single-Cell Expression Profiling of Dopaminergic Neurons Combined with Association Analysis Identifies Pyridoxal Kinase as Parkinson’s Disease Gene. Ann Neurol. 2009 Dec;66(6):792-8.	Elstner M, Morris CM, Heim K, Lichtner P, Bender A, Mehta D, Schulte C, Sharma M, Hudson G, Goldwurm S, Giovanetti A, Zeviani M, Burn DJ, McKeith IG, Perry RH, Jaros E, Krüger R, Wichmann HE, Schreiber S, Campbell H, Wilson JF, Wright AF, Dunlop M, Pistis G, Toniolo D, Chinnery PF, Gasser T, Klopstock T, Meitinger T, Prokisch H, Turnbull DM	15 Jan 2010	15th Jan 2010 Corresponding author was emailed Jan. 20, 2010 - Responded Jan 22 that data was still being analyzed for a future publication. Journal was contacted Feb 13. Managing editor responded and requested wording for policy and also contacted authors. Policy requiring microarray deposition adopted Feb. 26, 2010.
Thalamic transcriptome screening in three psychiatric states. J Hum Genet. 2009 Nov;54(11).(PMID: 19834500)	Chu TT, Liu Y, Kemether E	25 Mar 2010	Corresponding author was emailed March 29, 2010 - No response. Journal was emailed April 6, 2010.
The molecular classification of multiple myeloma. Blood. 2006 Sep 15;108(6):2020-8. PMID: 16728703; Gene-expression signature of benign monoclonal gammopathy evident in multiple myeloma is linked to good prognosis. Blood. 2007 Feb 15;109(4):1692-700. PMID: 17023574; Prognostic value of cyclin D2 mRNA expression in newly diagnosed multiple myeloma treated with high-dose chemotherapy and tandem autologous stem cell transplantations. Leukemia. 2006 Jul;20(7):1288-90. PMID: 16688228	Zhan F, Huang Y, Colla S, Stewart JP, Hanamura I, Gupta S, Epstein J, Yaccoby S, Sawyer J, Burington B, Anaissie E, Hollmig K, Pineda-Roman M, Tricot G, van Rhee F, Walker R, Zangari M, Crowley J, Barlogie B, Shaughnessy JD Jr.; Zhan F, Barlogie B, Arzoumanian V, Huang Y, Williams DR, Hollmig K, Pineda-Roman M, Tricot G, van Rhee F, Zangari M, Dhodapkar M, Shaughnessy JD Jr.; Hanamura I, Huang Y, Zhan F, Barlogie B, Shaughnessy J.	26 Mar 2010	Data is available in GEO (GSE2658) but does not include raw data (CEL files).Requires a Materials Transfer Agreement which is viewed as failing to meet Blood's policy. Journals were contacted April 7 and Blood's Peer Review Manager responded April 8 that steps are being taken to insure that the raw data are deposited appropriately.
Identification of differentially expressed genes in fibroblasts derived from patients with Dupuytren's Contracture. BMC Med Genomics. 2008 Apr 23;1:10. PMID: 18433489	Satish L, Laframboise WA, O'Gorman DB, Johnson S, Janto B, Gan BS, Baratz ME, Hu FZ, Post JC, Ehrlich GD, Kathju S.	1 Aor 2010	Corresponding author had initiated deposition at GEO but did not complete. Journal was contacted April 7. GEO followed up with author and obtained deposition (GSE21221) but is still waiting on raw data. Journal Scientific Editor responded April 23 that they are happy to contact the authors to encourage them to complete the deposition of their microarray in GEO.
Gene expression profiling in cluster headache: a pilot microarray study. Headache. 2006 Nov-Dec;46(10):1518-34. PMID: 17115985	Sjöstrand C, Duvefelt K, Steinberg A, Remahl IN, Waldenlind E, Hillert J.	7 Jun 2010	Corresponding author was emailed June 8. Journal was contacted June 15. Editor-in-Chief and Managing Editor responded June 21 requesting sample language for policy and will discuss at editorial board meeting. Author has responded Feb 15, 2011 and submission to ArrayExpress is in progress.