DeGNServer: Deciphering genome-scale gene networks through high performance reverse engineering analysis

BioMed Research International

Volumn 2013, Issue , 2013, Pages

  Li, Jun ^a   Wei, Hairong ^b,c   Zhao, Patrick Xuechun ^a  

^a PLANT BIOLOGY DIVISION   (United States)

^b MICHIGAN TECHNOLOGICAL UNIVERSITY   (United States)

^c Michigan Technological University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; EMBRYONIC STEM CELL; GENE REGULATORY NETWORK; GENETIC ALGORITHM; GENOME ANALYSIS; HEART DEVELOPMENT; HUMAN; MICROARRAY ANALYSIS; NONHUMAN; PLURIPOTENT STEM CELL; PREDICTION; SENSITIVITY AND SPECIFICITY; TISSUE MICROARRAY; WEB BROWSER; WORKFLOW; BIOLOGY; COMPUTER PROGRAM; DNA MICROARRAY; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENOME; INTERNET; METHODOLOGY; REVERSE GENETICS;

COMPUTATIONAL BIOLOGY; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; GENOME; INTERNET; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REVERSE GENETICS; SOFTWARE;

EID: 84891467279     PISSN: 23146133     EISSN: 23146141     Source Type: Journal    
DOI: 10.1155/2013/856325     Document Type: Article

References (60)

1. Parkinson H., Sarkans U., Shojatalab M., Abeygunawardena N., Contrino S., Coulson R., Farne A., Lara G. G., Holloway E., Kapushesky M., Lilja P., Mukherjee G., Oezcimen A., Rayner T., Rocca-Serra P., Sharma A., Sansone S., Brazma A., ArrayExpress-A public repository for microarray gene expression data at the EBI. Nucleic Acids Research 2005 33 D553 D555 2-s2.0-13444249955 10.1093/nar/gki056
2. Barrett T., Troup D. B., Wilhite S. E., Ledoux P., Rudnev D., Evangelista C., Kim I. F., Soboleva A., Tomashevsky M., Edgar R., NCBI GEO: mining tens of millions of expression profiles-database and tools update. Nucleic Acids Research 2007 35 1 D760 D765 2-s2.0-33846064113 10.1093/nar/gkl887
3. Wei H., Persson S., Mehta T., Srinivasasainagendra V., Chen L., Page G. P., Somerville C., Loraine A., Transcriptional coordination of the metabolic network in arabidopsis. Plant Physiology 2006 142 2 762 774 2-s2.0-33750063171 10.1104/pp.106.080358
4. Zhu X. L., Ai Z. H., Wang J., Xu Y. L., Teng Y. C., Weighted gene co-expression network analysis in identification of endometrial cancer prognosis markers. Asian Pacific Journal Cancer Prevention 2012 13 9 4607 4611
5. Presson A. P., Sobel E. M., Papp J. C., Suarez C. J., Whistler T., Rajeevan M. S., Vernon S. D., Horvath S., Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome. BMC Systems Biology 2008 2 article 95 2-s2.0-58549117328 10.1186/1752-0509-2-95
6. Nie J., Stewart R., Ruan F., Thomson J. A., Zhang H., Cui X., Wei H., TF-cluster: a pipeline for identifying functionally coordinated transcription factors via network decomposition of the Shared Coexpression Connectivity Matrix (SCCM). BMC Systems Biology 2011 5 article 53 2-s2.0-79955091925 10.1186/1752-0509-5-53
7. Kumari S., Stewart R., Nie J., Evaluation of gene association methods for coexpression network construction and biological knowledge discovery. PLoS ONE 2012 7 11 10.1371/journal.pone.0050411 e50411
8. Margolin A. A., Nemenman I., Basso K., Wiggins C., Stolovitzky G., Favera R. D., Califano A., ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 2006 7 supplement 1, article S7 2-s2.0-33947305781 10.1186/1471-2105-7-S1-S7
9. Faith J. J., Hayete B., Thaden J. T., Mogno I., Wierzbowski J., Cottarel G., Kasif S., Collins J. J., Gardner T. S., Large-scale mapping and validation of escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biology 2007 5 1, article e8 2-s2.0-34548289712 10.1371/journal.pbio.0050008
10. Li J., Wei H., Liu T., Zhao P. X., GPLEXUS: enabling genome-scale gene association network reconstruction and analysis for very large-scale expression data. Nucleic Acids Research 2013 10.1093/nar/gkt983
11. Li K.-C., Genome-wide coexpression dynamics: theory and application. Proceedings of the National Academy of Sciences of the United States of America 2002 99 26 16875 16880 2-s2.0-0037168518 10.1073/pnas.252466999
12. Horvath S., Dong J., Geometric interpretation of gene coexpression network analysis. PLoS Computational Biology 2008 4 8 2-s2.0-50949084896 10.1371/journal.pcbi.1000117 e1000117
13. Madar A., Greenfield A., Vanden-Eijnden E., Bonneau R., DREAM3: network inference using dynamic context likelihood of relatedness and the inferelator. PloS ONE 2010 5 3 e9803 10.1371/journal.pone.0009803
14. Nazri A., Lio P., Investigating meta-approaches for reconstructing gene networks in a mammalian cellular context. PLoS ONE 2012 7 1 2-s2.0-84855485205 10.1371/journal.pone.0028713 e28713
15. Xiong J., Yuan D., Fillingham J. S., Garg J., Lu X., Chang Y., Liu Y., Fu C., Pearlman R. E., Miao W., Gene network landscape of the ciliate tetrahymena thermophila. PLoS ONE 2011 6 5 2-s2.0-79957560183 10.1371/journal.pone.0020124 e20124
16. Michoel T., de Smet R., Joshi A., van de Peer Y., Marchal K., Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks. BMC Systems Biology 2009 3 article 49 2-s2.0-66449116353 10.1186/1752-0509-3-49
17. Wang D., Zhang C., Hearn D. J., Kang I.-H., Punwani J. A., Skaggs M. I., Drews G. N., Schumaker K. S., Yadegari R., Identification of transcription-factor genes expressed in the arabidopsis female gametophyte. BMC Plant Biology 2010 10 article 110 2-s2.0-77953491224 10.1186/1471-2229-10-110
18. Osorno R., Chambers I., Transcription factor heterogeneity and epiblast pluripotency. Philosophical Transactions of the Royal Society B 2011 366 article 1575 2230 2237 2-s2.0-79960058253 10.1098/rstb.2011.0043
19. Linnekin D., Park L. S., Farrar W. L., Dissociation of human cytokine receptor expression and signal transduction. Blood 1992 80 8 1896 1904 2-s2.0-0026787603
20. Edwards S., Elements of information theory, 2nd edition. Information Processing & Management 2008 44 1 400 401
21. Hu X., Wu F.-X., Mining and state-space modeling and verification of sub-networks from large-scale biomolecular networks. BMC Bioinformatics 2007 8 article 324 2-s2.0-38649114712 10.1186/1471-2105-8-324
22. Aluru M., Zola J., Nettleton D., Aluru S., Reverse engineering and analysis of large genome-scale gene networks. Nucleic Acids Research 2013 41 1, article e24
23. Wilcox R. R., A note on the Theil-Sen regression estimator when the regresser is random and the error term is heteroscedastic. Biometrical Journal 1998 40 3 261 268 2-s2.0-0032373378
24. Lyakhov I. G., Krishnamachari A., Schneider T. D., Discovery of novel tumor suppressor p53 response elements using information theory. Nucleic Acids Research 2008 36 11 3828 3833 2-s2.0-46349085558 10.1093/nar/gkn189
25. Reshef D. N., Reshef Y. A., Finucane H. K., Grossman S. R., McVean G., Turnbaugh P. J., Lander E. S., Mitzenmacher M., Sabeti P. C., Detecting novel associations in large data sets. Science 2011 334 6062 1518 1524 2-s2.0-83755163018 10.1126/science.1205438
26. Kohl M., Wiese S., Warscheid B., Cytoscape: software for visualization and analysis of biological networks. Methods in Molecular Biology 2011 696 291 303 2-s2.0-79952202448
27. van den Bulcke T., van Leemput K., Naudts B., van Remortel P., Ma H., Verschoren A., de Moor B., Marchal K., SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms. BMC Bioinformatics 2006 7 article 43 2-s2.0-33144486498 10.1186/1471-2105-7-43
28. Baldi P., Brunak S., Chauvin Y., Andersen C. A. F., Nielsen H., Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 2000 16 5 412 424 2-s2.0-0033931867
29. Irizarry R. A., Hobbs B., Collin F., Beazer-Barclay Y. D., Antonellis K. J., Scherf U., Speed T. P., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003 4 2 249 264 2-s2.0-0142121516
30. Yu J., Vodyanik M. A., Smuga-Otto K., Antosiewicz-Bourget J., Frane J. L., Tian S., Nie J., Jonsdottir G. A., Ruotti V., Stewart R., Slukvin I. I., Thomson J. A., Induced pluripotent stem cell lines derived from human somatic cells. Science 2007 318 5858 1917 1920 2-s2.0-36749043230 10.1126/science. 1151526
31. Watabe T., Roles of Dppa2 in the regulation of the present status and future of pluripotent stem cells. Journal of Biochemistry 2012 152 1 1 3 10.1093/jb/mvs057
32. Chan Y. S., Göke J., Lu X., A PRC2-dependent repressive role of PRDM14 in human embryonic stem cells and induced pluripotent stem cell reprogramming. Stem Cells 2012 31 4 682 692
33. Barbaric I., Harrison N. J., Rediscovering pluripotency: from teratocarcinomas to embryonic stem cells. Cardiff, 10-12 October 2011. The International Journal of Developmental Biology 2012 56 4 197 206 10.1387/ijdb.123503ib
34. Ramos P. S., Sajuthi S., Langefeld C. D., Immune function genes CD99L2, JARID2 and TPO show association with autism spectrum disorder. Molecular Autism 2012 3 1, article 4 10.1186/2040-2392-3-4
35. Boyer L. A., Tong I. L., Cole M. F., Johnstone S. E., Levine S. S., Zucker J. P., Guenther M. G., Kumar R. M., Murray H. L., Jenner R. G., Gifford D. K., Melton D. A., Jaenisch R., Young R. A., Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 2005 122 6 947 956 2-s2.0-25144525014 10.1016/j.cell.2005.08.020
36. Calloni R., Cordero E. A., Henriques J. A., Bonatto D., Reviewing and updating the major molecular markers for stem cells. Stem Cells and Development 2013 22 9 1455 1476 10.1089/scd.2012.0637
37. Kim M., Kang T.-W., Lee H.-C., Han Y.-M., Kim H., Shin H. D., Cheong H. S., Lee D., Kim S.-Y., Kim Y. S., Identification of DNA methylation markers for lineage commitment of in vitro hepatogenesis. Human Molecular Genetics 2011 20 14 2722 2733 2-s2.0-79959808342 10.1093/hmg/ddr171
38. Persson S., Wei H., Milne J., Page G. P., Somerville C. R., Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proceedings of the National Academy of Sciences of the United States of America 2005 102 24 8633 8638 2-s2.0-20844445318 10.1073/pnas.0503392102
39. Srivastava D., Making or breaking the heart: from lineage determination to morphogenesis. Cell 2006 126 6 1037 1048 2-s2.0-33748621746 10.1016/j.cell.2006.09.003
40. Vincentz J. W., Barnes R. M., Firulli B. A., Conway S. J., Cooperative interaction of Nkx2.5 and Mef2c transcription factors during heart development. Developmental Dynamics 2008 237 12 3809 3819 2-s2.0-57149103137 10.1002/dvdy.21803
41. Prall O. W. J., Menon M. K., Solloway M. J., Watanabe Y., Zaffran S., Bajolle F., Biben C., McBride J. J., Robertson B. R., Chaulet H., Stennard F. A., Wise N., Schaft D., Wolstein O., Furtado M. B., Shiratori H., Chien K. R., Hamada H., Black B. L., Saga Y., Robertson E. J., Buckingham M. E., Harvey R. P., An Nkx2-5/Bmp2/Smad1 negative feedback loop controls heart progenitor specification and proliferation. Cell 2007 128 5 947 959 2-s2.0-33847344204 10.1016/j.cell.2007.01.042
42. Takeda M., Briggs L. E., Wakimoto H., Marks M. H., Warren S. A., Lu J. T., Weinberg E. O., Robertson K. D., Chien K. R., Kasahara H., Slow progressive conduction and contraction defects in loss of Nkx2-5 mice after cardiomyocyte terminal differentiation. Laboratory Investigation 2009 89 9 983 993 2-s2.0-69349086498 10.1038/labinvest.2009.59
43. Lyons I., Parsons L. M., Hartley L., Li R., Andrews J. E., Robb L., Harvey R. P., Myogenic and morphogenetic defects in the heart tubes of murine embryos lacking the homeo box gene Nkx2-5. Genes and Development 1995 9 13 1654 1666 2-s2.0-0029090829
44. Nowotschin S., Liao J., Gage P. J., Epstein J. A., Campione M., Morrow B. E., Tbx1 affects asymmetric cardiac morphogenesis by regulating Pitx2 in the secondary heart field. Development 2006 133 8 1565 1573 2-s2.0-33646706385 10.1242/dev.02309
45. Théveniau-Ruissy M., Dandonneau M., Mesbah K., Ghez O., Mattei M.-G., Miquerol L., Kelly R. G., The del22q11.2 candidate gene Tbx1 controls regional outflow tract identity and coronary artery patterning. Circulation Research 2008 103 2 142 148 2-s2.0-48849103985 10.1161/CIRCRESAHA.108.172189
46. Zhang Z., Baldini A., In vivo response to high-resolution variation of Tbx1 mRNA dosage. Human Molecular Genetics 2008 17 1 150 157 2-s2.0-37549052138 10.1093/hmg/ddm291
47. Merscher S., Funke B., Epstein J. A., Heyer J., Puech A., Lu M. M., Xavier R. J., Demay M. B., Russell R. G., Factor S., Tokooya K., Jore B. S., Lopez M., Pandita R. K., Lia M., Carrion D., Xu H., Schorle H., Kobler J. B., Scambler P., Wynshaw-Boris A., Skoultchi A. I., Morrow B. E., Kucherlapati R., TBX1 is responsible for cardiovascular defects in velo-cardio-facial/DiGeorge syndrome. Cell 2001 104 4 619 629 2-s2.0-17744395906 10.1016/S0092-8674(01) 00247-1
48. Risebro C. A., Searles R. G., Melville A. A. D., Ehler E., Jina N., Shah S., Pallas J., Hubank M., Dillard M., Harvey N. L., Schwartz R. J., Chien K. R., Oliver G., Riley P. R., Prox1 maintains muscle structure and growth in the developing heart. Development 2009 136 3 495 505 2-s2.0-64549159888 10.1242/dev.030007
49. Risebro C. A., Petchey L. K., Smart N., Epistatic rescue of Nkx2. 5 adult cardiac conduction disease phenotypes by prospero-related homeobox protein 1 and HDAC3. Circulation Research 2012 111 2 e19 e31 10.1161/CIRCRESAHA.111.260695
50. Song K., Backs J., McAnally J., Qi X., Gerard R. D., Richardson J. A., Hill J. A., Bassel-Duby R., Olson E. N., The transcriptional coactivator CAMTA2 stimulates cardiac growth by opposing class II histone deacetylases. Cell 2006 125 3 453 466 2-s2.0-33646144852 10.1016/j.cell.2006.02.048
51. Lickert H., Takeuchi J. K., Von Both I., Walls J. R., McAuliffe F., Adamson S. L., Henkelman R. M., Wrana J. L., Rossant J., Bruneau B. G., Baf60c is essential for function of BAF chromatin remodelling complexes in heart development. Nature 2004 432 7013 107 112 2-s2.0-8544270889 10.1038/nature03071
52. Miller S. A., Mohn S. E., Weinmann A. S., Jmjd3 and UTX play a demethylase-independent role in chromatin remodeling to regulate t-box family member-dependent gene expression. Molecular Cell 2010 40 4 594 605 2-s2.0-78649263390 10.1016/j.molcel.2010.10.028
53. Tian Y., Yuan L., Goss A. M., Wang T., Yang J., Lepore J. J., Zhou D., Schwartz R. J., Patel V., Cohen E. D., Morrisey E. E., Characterization and in vivo pharmacological rescue of a Wnt2-Gata6 pathway required for cardiac inflow tract development. Developmental Cell 2010 18 2 275 287 2-s2.0-76549113391 10.1016/j.devcel.2010.01.008
54. Wang D.-Z., Chang P. S., Wang Z., Sutherland L., Richardson J. A., Small E., Krieg P. A., Olson E. N., Activation of cardiac gene expression by myocardin, a transcriptional cofactor for serum response factor. Cell 2001 105 7 851 862 2-s2.0-0035967868 10.1016/S0092-8674(01)00404-4
55. Wu J., Zhou D., Deng C., Wu X., Long L., Xiong Y., Characterization of porcine ENO3: genomic and cDNA structure, polymorphism and expression. Genetics Selection Evolution 2008 40 5 563 579 2-s2.0-50049090276 10.1051/gse:2008015
56. Li X., Tu L., Murphy P. G., Kadono T., Steeber D. A., Tedder T. F., CHST1 and CHST2 sulfotransferase expression by vascular endothelial cells regulates shear-resistant leukocyte rolling via L-selectin. Journal of Leukocyte Biology 2001 69 4 565 574 2-s2.0-0035071302
57. Li X., Tedder T. F., CHST1 and CHST2 sulfotransferases expressed by human vascular endothelial cells: cDNA cloning, expression, and chromosomal localization. Genomics 1999 55 3 345 347 2-s2.0-0033082291 10.1006/geno.1998. 5653
58. Hibuse T., Maeda N., Nakatsuji H., Tochino Y., Fujita K., Kihara S., Funahashi T., Shimomura I., The heart requires glycerol as an energy substrate through aquaporin 7, a glycerol facilitator. Cardiovascular Research 2009 83 1 34 41 2-s2.0-67649373933 10.1093/cvr/cvp095
59. Gambert S., Héliès-Toussaint C., Grynberg A., Regulation of intermediary metabolism in rat cardiac myocyte by extracellular glycerol. Biochimica et Biophysica Acta 2005 1736 2 152 162 2-s2.0-24344492092 10.1016/j.bbalip.2005.08.004
60. Ting M.-C., Wu N. L., Roybal P. G., Sun J., Liu L., Yen Y., Maxson R. E. Jr., EphA4 as an effector of Twist1 in the guidance of osteogenic precursor cells during calvarial bone growth and in craniosynostosis. Development 2009 136 5 855 864 2-s2.0-65549099259 10.1242/dev.028605