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Discovering tightly regulated and differentially expressed gene sets in whole genome expression data
2007
Bioinformatics
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We present a new method based on notions of tight regulation and differential expression to look for sets of genes which appear to be significantly affected by genetic variation. ...
Motivation: Recently, a new type of expression data is being collected which aims to measure the effect of genetic variation on gene expression in pathways. ...
Significant mouse hematopoietic stem cell gene sets Whole genome expression data e89 ...
doi:10.1093/bioinformatics/btl315
pmid:17237110
fatcat:kngz5ccvcffhdcdjg5b3zexrge
The Ets Transcription Factor EHF as a Regulator of Cornea Epithelial Cell Identity
2013
Journal of Biological Chemistry
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Over 10,000 genes are differentially regulated in the mouse cornea across the time course, showing dynamic expression during development and modest expression changes in fewer genes during aging. ...
Furthermore, this comprehensive gene expression data set for the cornea is a powerful tool for discovery of novel cornea regulators and pathways. ...
Acknowledgments We thank the University of California Irvine Genomics High-Throughput Facility for work on the whole genome expression arrays and sequencing. ...
doi:10.1074/jbc.m113.504399
pmid:24142692
pmcid:PMC3843046
fatcat:olhopkt3pzcfhlyck3trdgblhi
Dzip3 regulates developmental genes in mouse embryonic stem cells by reorganizing 3D chromatin conformation
2015
Scientific Reports
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Here, we tested whether known H2A ubiquitin ligases and deubiquitylases are involved in mES cell regulation and discovered that Dzip3, the E3 ligase of H2AK119, represses differentiation-inducible genes ...
We found that Dzip3 represses gene expression by orchestrating changes in 3D organization, in addition to regulating ubiquitylation of H2A. ...
Hiromi Hayashida for helpful discussions and technical support.
Author Contributions ...
doi:10.1038/srep16567
pmid:26568260
pmcid:PMC4645096
fatcat:bgyxrbssbfgkbhrvjkcw46drne
White Blood Cell Differentials Enrich Whole Blood Expression Data in the Context of Acute Cardiac Allograft Rejection
2012
Bioinformatics and Biology Insights
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We identified eight differentially expressed probe-sets significantly correlated to monocytes (mapping to 6 genes, all down-regulated in ARs versus NRs) at a false discovery rate (FDR) # 15%. ...
None of the genes identified are present in a biomarker panel of acute heart rejection previously published by our group and discovered in the same data. ...
Grateful acknowledgment also for funding from Genome Canada, Novartis Pharma AG, IBM, Genome British Columbia and the NCE CECR PROOF Centre of Excellence. ...
doi:10.4137/bbi.s9197
pmid:22550401
pmcid:PMC3329187
fatcat:tbhnjkyptfgi5b6cf4xxwpz3au
Biological Specifications for a Synthetic Gene Expression Data Generation Model
[chapter]
2006
Lecture Notes in Computer Science
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An open problem in gene expression data analysis is the evaluation of the performance of gene selection methods applied to discover biologically relevant sets of genes. ...
The natural solution to this problem consists in developing an artificial model to generate gene expression data, in order to know in advance the set of biologically relevant genes. ...
Differential expression analysis of single genes, even if it may be useful to identify specific genes involved in biological processes [12] , cannot capture the complexity of tightly regulated processes ...
doi:10.1007/11676935_34
fatcat:kepbib4zm5ab7pgyoshtfs676q
Semi-supervised gene shaving method for predicting low variation biological pathways from genome-wide data
2009
BMC Bioinformatics
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Using available pathway gene sets as prior knowledge, whether complete or incomplete, our algorithm is capable of forming tightly regulated gene clusters showing modest variation across samples. ...
However, gene expression in many signaling pathways show only modest and concordant changes that fail to be identified by these methods. ...
The data set consists of whole yeast genome expression profiles interrogated over two full cell cycles (20 evenly spaced time points) synchronized by elutriation. ...
doi:10.1186/1471-2105-10-s1-s54
pmid:19208157
pmcid:PMC2648790
fatcat:ubkatzxlhbdahcwrp75mxrzkoa
Searching for the Molecular Pathways Regulating Bone Mineral Density in the Proteome and RNA Interference Era
2013
Journal of Orthopedics & Rheumatology
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In this review, current methods employed to identify genes involved in osteoporosis, which include linkage analysis, candidate gene association studies, genome wide association studies, transcriptome microarray ...
The complex processes of bone matrix mineralization and bone remodeling are tightly regulated by several transcription factors and signal transduction pathways. ...
Proteomics: The proteome represents the whole set of proteins that are expressed in a given cell under certain conditions. ...
doi:10.13188/2334-2846.1000004
fatcat:27singmgi5atdkhoxilwdmgjem
Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses
2008
Proceedings of the National Academy of Sciences of the United States of America
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Whole-genome oligonucleotide tiling arrays and tandem mass spectrometry identified transcripts for >8,000 genes, Ϸ3,000 of which were not previously described and included noncoding and antisense RNAs. ...
Gene-specific expression profiles detected a set of 75 genes induced only under low concentrations of silicon but not under low concentrations of nitrogen or iron, alkaline pH, or low temperatures. ...
We thank Igor Grigoriev and Bobby Otillar from the Joint Genome Institute for useful discussions. We also thank Drs. Amy ...
doi:10.1073/pnas.0707946105
pmid:18212125
pmcid:PMC2234187
fatcat:ncnflfcdlnde5g7jqf2pydlcma
Identification of candidate genes and natural allelic variants for QTLs governing plant height in chickpea
2016
Scientific Reports
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protein, malic oxidoreductase, NADH dehydrogenase iron-sulfur protein, expressed protein and bZIP transcription factor) regulating plant height in chickpea. ...
Overall, combining high-resolution QTL mapping with genetic association analysis and differential expression profiling, delineated natural allelic variants in five candidate genes (encoding cytochromec-biosynthesis ...
Alice Kujur acknowledges the CSIR (Council of Scientific and Industrial Research) for Senior Research Fellowship award. ...
doi:10.1038/srep27968
pmid:27319304
pmcid:PMC4913251
fatcat:c2w36d76cvdk3i375ibmdd3bgi
A Scalable Approach for Discovering Conserved Active Subnetworks across Species
2010
PLoS Computational Biology
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We applied our cross-species approach to identify conserved modules that are differentially active in stem cells relative to differentiated cells based on parallel gene expression studies and functional ...
We assess the statistical significance of the subnetworks by comparing them with subnetworks discovered on random permutations of the differential expression data. ...
The only gene in the whole subnetwork that is found to be up-regulated in mouse and human pluripotent stem cells is LCK ( Figure 5D ). ...
doi:10.1371/journal.pcbi.1001028
pmid:21170309
pmcid:PMC3000367
fatcat:73pzlrjts5dxdcwt3htf2chsai
Profiling chromatin accessibility responses in human neutrophils with sensitive pathogen detection
2021
Life Science Alliance
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We identify three classes of gene regulation, chromatin access changes in the promoter; changes in the promoter and distal enhancers; and controlling expression through changes solely in distal enhancers ...
Epigenomic changes are plastic, only ∼120 are shared by E. coli challenges over time, resulting in varied differential genes and associated processes. ...
Acknowledgements We would like to thank the Stanford Functional Genomics Facility for performing the sequencing carried out in this study. ...
doi:10.26508/lsa.202000976
pmid:34145026
pmcid:PMC8321655
fatcat:l25qpgfjkngvzc7gvvhkd7tvjm
High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA–tRNA interface
2014
Genome Research
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We discovered that mRNA codon pools are highly stable over development and simply reflect the genomic background; in contrast, precise regulation of tRNA gene families is required to create the corresponding ...
Here, we characterized the expression of mRNA and tRNA genes quantitatively at multiple time points in two developing mouse tissues. ...
Acknowledgments We thank the CI Biological Resource Unit and Genomics Cores for technical support; Gordon Brown, Tim Rayner, Margus Lukk, and Robert Sugar for data analysis assistance; Kristian Vlahovicek ...
doi:10.1101/gr.176784.114
pmid:25122613
pmcid:PMC4216921
fatcat:5pypsmvdtzay7ovgtcb5tbdpji
A STORY OF GROWING CONFUSION: GENES AND THEIR REGULATION
2008
BIOMAT 2007
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The complexity of the transcriptome and the prevalence of noncoding transcripts forces us to reconsider both the concept of the "gene" itself and our understanding of the mechanisms that regulate "gene ...
High-throughput experiments have produced convicing evidence for an extensive contribution of diverse classes of RNAs in the expression of genetic information. ...
Acknowledgments PFS acknowledges the hospitality of the EFG @ ASU in September 2007, where part of this work was conceived. ...
doi:10.1142/9789812812339_0017
fatcat:btdhkk3vwrfprlacmsppna3yyy
A STORY OF GROWING CONFUSION: GENES AND THEIR REGULATION
2008
Biophysical Reviews and Letters
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The complexity of the transcriptome and the prevalence of noncoding transcripts forces us to reconsider both the concept of the "gene" itself and our understanding of the mechanisms that regulate "gene ...
High-throughput experiments have produced convicing evidence for an extensive contribution of diverse classes of RNAs in the expression of genetic information. ...
Acknowledgments PFS acknowledges the hospitality of the EFG @ ASU in September 2007, where part of this work was conceived. ...
doi:10.1142/s1793048008000757
fatcat:umxkcels4neqng27bcbx625iem
microRNAs contribute to enhanced salt adaptation of the autopolyploid Hordeum bulbosum compared with its diploid ancestor
2017
The Plant Journal
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Whole genome duplication can result in the expansion of miRNA families, and the innovative miRNA-target interaction is vital for adaptive response to various environments. ...
Of these, miR528b-3p was only detected in the tetraploid plants, and down -regulated in salt stress tetraploid plants relative to that in tetraploid check (CK). ...
expression change of a whole genome in one shot, genome-wide gene expression has been studied in many allopolyploids, including Arabidopsis, Cotton, Senecio and Wheat. ...
doi:10.1111/tpj.13546
pmid:28370696
fatcat:xwanf4dcs5czrkep2ryexgbb3u
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