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Series GSE54710 Query DataSets for GSE54710
Status Public on Feb 05, 2014
Title MicroRNAs and their target genes in gingival tissues.
Organism Homo sapiens
Experiment type Non-coding RNA profiling by array
Summary To gain insights into the in vivo function of miRNAs in the context of periodontitis, we examined the occurrence of miRNAs in healthy and diseased gingival tissues and validated their in silico-predicted targets through mRNA profiling using whole-genome microarrays in the same specimens. Eighty-six individuals with periodontitis contributed 198 gingival papillae: 158 'diseased' (bleeding-on-probing, PD > 4 mm, and AL ≥ 3 mm) and 40 'healthy' (no bleeding, PD ≤ 4 mm, and AL ≤ 2 mm). Expression of 1,205 miRNAs was assessed by microarrays, followed by selected confirmation by quantitative RT-PCR. Predicted miRNA targets were identified and tested for enrichment by Gene Set Enrichment Analysis (GSEA). Enriched gene sets were grouped in functional categories by DAVID and Ingenuity Pathway Analysis. One hundred fifty-nine miRNAs were significantly differentially expressed between healthy and diseased gingiva. Four miRNAs (hsa-miR-451, hsa-miR-223, hsa-miR-486-5p, hsa-miR-3917) were significantly overexpressed, and 7 (hsa-miR-1246, hsa-miR-1260, hsa-miR-141, hsa-miR-1260b, hsa-miR-203, hsa-miR-210, hsa-miR-205*) were underexpressed by > 2-fold in diseased vs. healthy gingiva. GSEA and additional filtering identified 60 enriched miRNA gene sets with target genes involved in immune/inflammatory responses and tissue homeostasis. This is the first study that concurrently examined miRNA and mRNA expression in gingival tissues and will inform mechanistic experimentation to dissect the role of miRNAs in periodontal tissue homeostasis and pathology.
 
Overall design The dataset comprise 200 gingival tissue samples from 86 patients with periodontitis. All samples are included in this series, but 2 where not included in the study, as they did not pass our QC. Each patient has one or more healthy and disease sample and samples can be of chronic or aggressive periodontitis type.
 
Contributor(s) Stoecklin-Wasmer C, Guarnieri P, Celenti R, Demmer RT, Kebschull M, Papapanou PN
Citation(s) 22879578
Submission date Feb 05, 2014
Last update date Feb 06, 2014
Contact name Paolo Guarnieri
E-mail(s) p.guarnieri@hotmail.com
Organization name Columbia University
Department Systems Biology
Street address 1130 St. Nicholas Avenue
City New York
State/province NY
ZIP/Postal code 10032
Country USA
 
Platforms (1)
GPL15159 Agilent-031181 Unrestricted_Human_miRNA_V16.0_Microarray 030840 (Probe Name version)
Samples (200)
GSM1322472 P5S1L1H1: ChronicLocalizedControl
GSM1322473 P5S2L1H1: ChronicLocalizedAffected
GSM1322474 P5S3L1H1: ChronicLocalizedAffected
Relations
BioProject PRJNA237462

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE54710_RAW.tar 1.6 Gb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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