Key words: Microarray Data format Tab delimited MIAME
Minimum information about a microarray experiment (MIAME
)--Successes, failures, challenges.
 Nonstandard abbreviations: CTCs, circulating tumor cells; MIAME
, minimal information about microarray experiment; GEO, gene expression Omnibus; AGCC, Affymetrix GeneChip Command Console software; SAM, significance analysis of microarray; FDR, false discovery rate; FC, fold change; PCA, principal component analysis; IPA, ingenuity pathway analysis; TAC, transcriptome analysis console; RT, reverse transcription; qPCR, quantitative PCR; DETs, differentially expressed transcripts; hESCs, human embryonic stem cells; FA, fanconi anemia; PSCs, pluripotentstem cells; GLS2, glutaminase 2; CBS, cystathionine-,8-synthase; CTH, cystathionine-y-lyase.
 Nonstandard abbreviations: FDA, US Food and Drug Administration; NCI, National Cancer Institute; ICTRP, International Clinical Trials Registry Platform; ICMJE, International Committee of Medical Journal Editors; HUGO, Human Gene Organisation; TKI, tyrosine kinase inhibitor; CTBS, Clinical Trials Biomarkers Standards; FGED, Functional Genomics Data Society; MGED, Microarray Gene Expression Data Society; MIAME
, minimum information needed to describe a microarray experiment; REMARK, Reporting recommendations for tumor MARKer; BRISQ, biospecimen reporting for improved study quality; API, application programming interface; HGNC, HUGO Gene Nomenclature Committee; HGVS, Human Genome Variation Society; regex, regular expression; RESTful, REpresentational State Transfer.
All data is MIAME
compliant, and the raw data has been deposited in GEO (accession number: GSE31685), a MIAME-compliant database.
These include the MIAME
(Minimum Information about a Microarray Experiment) conventions for reporting microarray data, the CEBS (Chemical Effects in Biological Systems) database standards, and the developing SEND (Standard for Exchange of Nonclinical Data) standards for reporting preclinical safety data.
Poor access to data motivated the 2001 MIAME
(minimum information about a microarray experiment) standards in the first place (2).
The raw data from the microarray experiment, comprising of the chip details and normalized signal intensity has been submitted to Gene expression omnibus (GEO) database at NCBI as per the guidelines and templates advised by MIAME
For publication of research that involves array technology, mandatory full data deposition is already the norm, based on the Minimum Information About a Microarray Experiment (MIAME
) (2) standard (5).
Manuscripts submitted the fields of toxicogenomics, pharmacogenomics, proteomics, metabolomics, metabonomics, molecular epidemiology, translational aspects of genomic research, and molecular medicine must follow the guidelines based on "Minimum Information About a Microarray Experiment - MIAME
," developed by the Microarray Gene Expression Data Society (http://www.mged.org/miame).
This problem is exacerbated by the fact that the current standard [Minimum Information about a Microarray Experiment (MIAME
) (19)] uses just 1 unstructured text field to store sample characteristics (response and so forth).
The NPSC evaluated the content of the mock submissions using the framework for reporting microarray data outlined by the Microarray Gene Expression Data (MGED) Society in their proposals of the minimum information about a microarray experiment (MIAME
) (Brazma et al.