Comment[ArrayExpressAccession]	E-GEOD-49875
MAGE-TAB Version	1.1				
Public Release Date	2013-08-15
Investigation Title	HuMiChip analysis of Saliva microbiota				
Comment[Submitted Name]	HuMiChip analysis of Saliva microbiota
Experiment Description	Human saliva microbiota is phylogenetically divergent among host individuals yet their roles in health and disease are poorly appreciated. We employed a microbial functional gene microarray, HuMiChip 1.0, to reconstruct the global functional profiles of human saliva microbiota from ten healthy and ten caries-active adults. Saliva microbiota in the pilot population featured a vast diversity of functional genes. No significant distinction in gene number or diversity indices was observed between healthy and caries-active microbiota. However, co-presence network analysis of functional genes revealed that caries-active microbiota was more divergent in non-core genes than healthy microbiota, despite both groups exhibited a similar degree of conservation at their respective core genes. Furthermore, functional gene structure of saliva microbiota could potentially distinguish caries-active patients from healthy hosts. Microbial functions such as Diaminopimelate epimerase, Prephenate dehydrogenase, Pyruvate-formate lyase and N-acetylmuramoyl-L-alanine amidase were significantly linked to caries. Therefore, saliva microbiota carried disease-associated functional signatures, which could be potentially exploited for caries diagnosis.  The DMFT INDEX (Decayed, Missing, Filled [DMF] teeth index used in dental epidemiology) values are provided for each sample We employed a microbial functional gene microarray, HuMiChip 1.0, to reconstruct the global functional profiles of human saliva microbiota from ten healthy and ten caries-active adults.				
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl			
Person Last Name	Tu				
Person First Name	Qichao				
Person Email	philloid@gmail.com				
Person Affiliation	University of Oklahoma				
Person Address	University of Oklahoma, 101 David L Boren Blvd, Norman, OK, USA				
Person Roles	submitter				
Protocol Name	P-GSE49875-1	P-GSE49875-3	P-GSE49875-4	P-GSE49875-2	P-GSE49875-5
Protocol Description	The data processing and analysis was carried out by the IEG microarray manager available at http://ieg.ou.edu/microarray/, which is a data analysis pipeline specifically designed for functional gene arrays such as GeoChip and HuMiChip etc. Data was filtered by SNR<=2, minimal signal intensity>=1000, resulting incomplete/subset data matrix (Probes which did not meet these criteria were not considered as detected in the study). Signal intensity were normalized by CORS universal standard probes (Liang et. al 2010 AEM), probes with SNR<2 are removed, all data was log transformed and mean ratio was calculated for further statistical analysis We used minimal signal intensity of 1000 and SNR (Signal to Noise Ratio) cutoff of 2 for positive callings of the presence of a gene ID_REF =  VALUE = mean ratio of normalized log transformed signal to noise intensity	DNA was labeled with the fluorescent dye Cy5 (GE Healthcare) by random priming	DNA was suspended in hybridization buffer and then kept at 65°C until hybridization. Hybridizations were performed at 42°C for 10 h using a Tecan HS4800 Pro hybridization station	Two milliliters of saliva were collected from each human-host individual into a tube containing an equal volume of lysis buffer and followed by DNA extraction	Arrays were scanned with a ScanArray 500 microarray scanner at 633 nm using a laser power of 90% and a photomultiplier tube (PMT) gain of 75%.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	DMFT INDEX	AGE	SEX		
Experimental Factor Type	dmft index	age	sex		
Comment[SecondaryAccession]	GSE49875				
Comment[GEOReleaseDate]	2013-08-15				
Comment[ArrayExpressSubmissionDate]	2013-08-14				
Comment[GEOLastUpdateDate]	2013-08-17				
Comment[AEExperimentType]	comparative genomic hybridization by array				
SDRF File	E-GEOD-49875.sdrf.txt