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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

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)

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:

Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density

Relations

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

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 7�replicate1	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 7�replicate2	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 7�replicate3	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 17�replicate1	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 17�replicate2	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 &7�replicate3	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)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE158147_GSE2332_Unsorted_Osteoblast_7_17days.xlsx	1.1 Mb	(ftp)(http)	XLSX
Processed data are available on Series record

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