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Series GSE158147 Query DataSets for GSE158147
Status Public on Jan 12, 2021
Title Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density [Unsorted_Osteoblast_7_17days]
Sample organism Mus musculus
Experiment type Expression profiling by array
Third-party reanalysis
Summary The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored the International Mouse Phenotyping Consortium (IMPC) for the analysis of skeletal data from 3,974 mutant strains for bone mineral density (BMD), a measure that is frequently altered in a range of bone pathologies including osteoporosis. A total of 200 genes were found to significantly affect BMD. This gene pool comprised 141 genes that were previously not known to have a function in bone biology and was complementary to pools derived from recent human studies. Nineteen of the 141 BMD genes also caused skeletal abnormalities. Further, evidence suggested a direct role for several of the identified BMD genes in osteoclasts and osteoblasts, and candidate genes for further investigation were prioritized. Overall, the results add novel pathophysiological and molecular insight into bone health and disease
 
Overall design We downloaded and re-analysed the gene expression profile of the datasets published by Kalajzic et al., (2005) PMID: 15834136 with GEO accession number GSE2332. We re-analysed only the Osteoblast precursors samples from 7 and 17 days of induction, to identify osteoblast specific genes and their expression levels to apply GeneNet Schaefer and Strimmer algorythm for learning large-scale gene association networks (http://www.strimmerlab.org/software/genenet/). This method allows to statistically assess the reliability of a given network (nodes and edges) using gene expression data to compute q-values and posterior probabilities for each potential edge connecting in a pairwise manner the nodes of the network we built in silico using REACTOME and STRING databases . Data pre-processing and annotation: The raw intensity measurements of the arrays downloaded from the GEO platform in .txt where normalized using limma Quantile based normalization algorithm producing the summaries at the probe/transcript level. The probes were gene and transcript annotated using the specific R package mgu74av2.db . Differential expression analysis (DEA): We carried on the differential expression analysis in R environment using limma. We provide the limma normalized expression data matrix to be used for GeneNet.
Web link https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009190
 
Contributor(s) Muñiz Moreno MM, Herault Y, Mayer-Kuckuk P, Hrabe de Angelis M
Citation(s) 33370286
Submission date Sep 17, 2020
Last update date Jan 12, 2021
Contact name maria del mar muñiz moreno
E-mail(s) munizmom@igbmc.fr
Organization name IGBMC
Department Translational medicine and neurogenetics
Lab Physiopathology of aneuploidy, gene dosage effect and Down syndrome - Yann Herault team
Street address 1 Rue Laurent Fries
City Strasbourg
State/province Alsace
ZIP/Postal code 67400
Country France
 
This SubSeries is part of SuperSeries:
GSE158151 Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density
Relations
Reanalysis of GSM43184
Reanalysis of GSM43205
Reanalysis of GSM43198
Reanalysis of GSM43191
Reanalysis of GSM43212
Reanalysis of GSM43219

subSeries_GSE2332_Unsorted_Osteoblast_7_17days header descriptions
GEO_GSE_ID
GEO_GSM_ID
Sample_name
title
Raw data file
source_name
organism
cell_type
cell_culture_induction
biosample
GEO_platform_id
chip_name

Data table
GEO_GSE_ID GEO_GSM_ID Sample_name title Raw data file source_name organism cell_type cell_culture_induction biosample GEO_platform_id chip_name
GSE2332 GSM43184 Unsorted_OsteoblastPrecursors_7days_1 Unsorted_OsteoblastPrecursors_7days_rep1 Not available from GEO Profiling FACS unsorted Calvarial Osteoblast Cultures: Day 7replicate1 Mus musculus mCOB cells 7 days Exp99Un on 74A GPL81 [MG_U74Av2] Affymetrix Murine Genome U74A Version 2 Array
GSE2332 GSM43205 Unsorted_OsteoblastPrecursors_7days_2 Unsorted_OsteoblastPrecursors_7days_rep2 Not available from GEO Profiling FACS unsorted Calvarial Osteoblast Cultures: Day 7replicate2 Mus musculus mCOB cells 7 days Exp103Un on 74A GPL81 [MG_U74Av2] Affymetrix Murine Genome U74A Version 2 Array
GSE2332 GSM43198 Unsorted_OsteoblastPrecursors_7days_3 Unsorted_OsteoblastPrecursors_7days_rep3 Not available from GEO Profiling FACS unsorted Calvarial Osteoblast Cultures: Day 7replicate3 Mus musculus mCOB cells 7 days Exp101Un on 74A GPL81 [MG_U74Av2] Affymetrix Murine Genome U74A Version 2 Array
GSE2332 GSM43191 Unsorted_OsteoblastPrecursors_17days_after_treatment_1 Unsorted_OsteoblastPrecursors_17days_after_treatment_rep1 Not available from GEO Profiling FACS unsorted Calvarial Osteoblast Cultures: Day 17replicate1 Mus musculus mCOB cells 17 days Exp100Un on 74A GPL81 [MG_U74Av2] Affymetrix Murine Genome U74A Version 2 Array
GSE2332 GSM43212 Unsorted_OsteoblastPrecursors_17days_after_treatment_2 Unsorted_OsteoblastPrecursors_17days_after_treatment_rep2 Not available from GEO Profiling FACS unsorted Calvarial Osteoblast Cultures: Day 17replicate2 Mus musculus mCOB cells 17 days Exp105Un on 74A GPL81 [MG_U74Av2] Affymetrix Murine Genome U74A Version 2 Array
GSE2332 GSM43219 Unsorted_OsteoblastPrecursors_17days_after_treatment_3 Unsorted_OsteoblastPrecursors_17days_after_treatment_rep3 Not available from GEO Profiling FACS unsorted Calvarial Osteoblast Cultures: Day &7replicate3 Mus musculus mCOB cells 17 days Exp106Un on 74A GPL81 [MG_U74Av2] Affymetrix Murine Genome U74A Version 2 Array

Total number of rows: 6


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
GSE158147_GSE2332_Unsorted_Osteoblast_7_17days.xlsx 1.1 Mb (ftp)(http) XLSX
Raw data not provided for this record
Processed data are available on Series record

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