Advancing the understanding of the embryo transcriptome co-regulation using meta-, functional, and gene network analysis tools

Reproduction - Tập 135 Số 2 - Trang 213-224 - 2008
Sandra L. Rodriguez‐Zas1, Yun Woong Ko2, Heather Adams2, Bruce R. Southey2
1Department of Animal Sciences, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
2University of Illinois at Urbana Champaign

Tóm tắt

Embryo development is a complex process orchestrated by hundreds of genes and influenced by multiple environmental factors. We demonstrate the application of simple and effective meta-study and gene network analyses strategies to characterize the co-regulation of the embryo transcriptome in a systems biology framework. A meta-analysis of nine microarray experiments aimed at characterizing the effect of agents potentially harmful to mouse embryos improved the ability to accurately characterize gene co-expression patterns compared with traditional within-study approaches. Simple overlap of significant gene lists may result in under-identification of genes differentially expressed. Sample-level meta-analysis techniques are recommended when common treatment levels or samples are present in more than one study. Otherwise, study-level meta-analysis of standardized estimates provided information on the significance and direction of the differential expression. Cell communication pathways were highly represented among the genes differentially expressed across studies. Mixture and dependence Bayesian network approaches were able to reconstruct embryo-specific interactions among genes in the adherens junction, axon guidance, and actin cytoskeleton pathways. Gene networks inferred by both approaches were mostly consistent with minor differences due to the complementary nature of the methodologies. The top–down approach used to characterize gene networks can offer insights into the mechanisms by which the conditions studied influence gene expression. Our work illustrates that further examination of gene expression information from microarray studies including meta- and gene network analyses can help characterize transcript co-regulation and identify biomarkers for the reproductive and embryonic processes under a wide range of conditions.

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Tài liệu tham khảo

1997, The Biochemical journal, 324, 523, 10.1042/bj3240523

2004, SEMINARS IN CELL AND DEVELOPMENTAL BIOLOGY, 15, 555, 10.1016/j.semcdb.2004.04.009

Bartsevich, 2003, Stem Cells, 21, 632, 10.1634/stemcells.21-6-632

Baum, 1999, Genes & Development, 13, 472, 10.1101/gad.13.4.472

1995, JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B, 57, 289

Berghella, 2005, Obstetrics & Gynecology, 106, 181, 10.1097/01.AOG.0000168435.17200.53

Berti, 2006, Neuromolecular medicine, 8, 191, 10.1385/NMM:8:1:191

Bolstad, 2004, International review of neurobiology, 60, 25, 10.1016/S0074-7742(04)60002-X

2005, 48, 77

Carey, 2007, Addictive behaviors, 32, 2469, 10.1016/j.addbeh.2007.05.004

Choi, 2003, Bioinformatics, 19, i84, 10.1093/bioinformatics/btg1010

Chowdhury, 1988, Nucleic Acids Research, 16, 9995, 10.1093/nar/16.21.9995

Druse, 2007, Brain research, 1150, 46, 10.1016/j.brainres.2007.02.092

2002, Annual review of pharmacology and toxicology, 42, 181, 10.1146/annurev.pharmtox.42.083001.110955

Friedman, 2000, Journal of computational biology : a journal of computational molecular cell biology, 7, 601, 10.1089/106652700750050961

2007, DEVELOPMENTAL DYNAMICS AN OFFICIAL PUBLICATION OF THE AMERICAN ASSOCIATION OF ANATOMISTS, 236, 613, 10.1002/dvdy.21048

Hailesellasse Sene, 2007, BMC genomics [electronic resource], 8, 85, 10.1186/1471-2164-8-85

1999, 89, 243

2006, INFORMATION SYSTEMS FRONTIERS, 8, 9, 10.1007/s10796-005-6099-z

1995, 90, 773, 10.1080/01621459.1995.10476572

Kerr, 2003, Journal of computational biology : a journal of computational molecular cell biology, 10, 891, 10.1089/106652703322756131

Lee, 1997, Biochemical and biophysical research communications, 240, 309, 10.1006/bbrc.1997.7655

2006, Bioinformatics, 22, 96, 10.1093/bioinformatics/bti752

Maunoury, 1992, Development, 115, 717, 10.1242/dev.115.3.717

Miller, 2006, Journal of neurochemistry, 97, 1182, 10.1111/j.1471-4159.2006.03858.x

2002, ENVIRONMENTAL TOXICOLOGY AND CHEMISTRYSETAC, 21, 2731, 10.1002/etc.5620211229

2002, INTERNATIONAL JOURNAL ON ARTIFICIAL INTELLIGENCE TOOLS, 11, 369, 10.1142/S0218213002000940

Nemeth, 2005, Toxicology and applied pharmacology, 206, 219, 10.1016/j.taap.2004.12.013

2005, Science Signaling, 281, pl4

Pe'er, 2001, Bioinformatics, 17, S215, 10.1093/bioinformatics/17.suppl_1.S215

2007, PNAS, 104, 12383, 10.1073/pnas.0705324104

Rhodes, 2002, Cancer Research, 62, 4427

2006, BMC genomics [electronic resource], 13, 233

Rodriguez-Zas, 2008, Reproduction, 135, 129, 10.1530/REP-07-0426

Rose, 1995, PNAS, 92, 6022, 10.1073/pnas.92.13.6022

2007, 133, 825

2002, 35, 907

Singh, 2005, Reproductive toxicology (Elmsford, N.Y.), 19, 421, 10.1016/j.reprotox.2004.11.008

Soleman, 2003, Birth defects research. Part A, Clinical and molecular teratology, 67, 98, 10.1002/bdra.10005

Suzuki, 2007, Experimental Biology and Medicine, 232, 503

Takahashi, 2005, Biochemical Society Transactions, 33, 1522, 10.1042/BST20051522

2006, Bioinformatics, 22, 2413, 10.1093/bioinformatics/btl396

2007, COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY PART B BIOCHEMISTRY AND MOLECULAR BIOLOGY, 146, 357, 10.1016/j.cbpb.2006.11.006

Wolfinger, 2001, Journal of computational biology : a journal of computational molecular cell biology, 8, 625, 10.1089/106652701753307520

Yu, 2001, Oncogene, 20, 3995, 10.1038/sj.onc.1204524

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Thông tin xuất bản

Reproduction

Tập 135 Số 2

213-224

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