Knowledge-based bioinformatics for the study of mammalian oocytes

International Journal of Developmental Biology

Volumn 56, Issue 10-12, 2012, Pages 859-866

  Mulas, Francesca ^a   Sacchi, Lucia ^a   Zagar, Lan ^b   Garagna, Silvia ^a   Zuccotti, Maurizio ^c   Zupan, Blaz ^a,b   Bellazzi, Riccardo ^a  

^a UNIVERSITY OF PAVIA   (Italy)

^b UNIVERSITY OF LJUBLJANA   (Slovenia)

^c UNIVERSITY OF PARMA   (Italy)

Author keywords

Database; Knowledge extraction; Oocyte; Stem cell

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; BIOINFORMATICS; CELL DIFFERENTIATION; CHEMICAL DATABASE; CHEMICAL STRUCTURE; COMPARATIVE STUDY; COMPUTER PROGRAM; DATA EXTRACTION; EMBRYO DEVELOPMENT; GENE EXPRESSION; GENE FUNCTION; GENE PRODUCT; GENETIC ASSOCIATION; GENETIC DATABASE; GENOME; INFORMATION DISSEMINATION; INFORMATION PROCESSING; KNOWLEDGE BASE; MAMMAL; MEDICAL LITERATURE; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; ONLINE SYSTEM; OOCYTE; OOCYTE DEVELOPMENT; OVARY FOLLICLE DEVELOPMENT; PRIORITY JOURNAL; TAXONOMY;

ANIMALS; CELL DIFFERENTIATION; COMPUTATIONAL BIOLOGY; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE REGULATORY NETWORKS; HUMANS; OOCYTES; OOGENESIS;

EID: 84873736865     PISSN: 02146282     EISSN: None     Source Type: Journal    
DOI: 10.1387/ijdb.120138fm     Document Type: Article

References (35)

1. AIBA, K., NEDOREZOV, T., PIAO, Y., NISHIYAMA, A., MATOBA, R., SHAROVA, L.V., SHAROV, A.A., YAMANAKA, S., NIWA, H. and KO, M.S. (2009). Defining developmental potency and cell lineage trajectories by expression profiling of differentiating mouse embryonic stem cells. DNA Res 16: 73-80.
2. AL-SHAHROUR, F., MINGUEZ, P., VAQUERIZAS, J.M., CONDE, L. and DOPAZO, J. (2005). BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. Nucleic Acids Res 33: W460-464.
3. ASHBURNER, M., BALL, C.A., BLAKE, J.A., BOTSTEIN, D., BUTLER, H., CHERRY, J.M., DAVIS, A.P., DOLINSKI, K., DWIGHT, S.S., EPPIG, J.T. et al., (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
4. BABAIE, Y., HERWIG, R., GREBER, B., BRINK, T.C., WRUCK, W., GROTH, D., LEHRACH, H., BURDON, T. and ADJAYE, J. (2007). Analysis of Oct4-dependent transcriptional networks regulating self-renewal and pluripotency in human embryonic stem cells. Stem Cells 25: 500-510.
5. BADER, G.D., BETEL, D. and HOGUE, C.W. (2003). BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res 31: 248-250.
6. CAMPBELL, P.A., PEREZ-IRATXETA, C., ANDRADE-NAVARRO, M.A. and RUD-NICKI, M.A. (2007). Oct4 targets regulatory nodes to modulate stem cell function. PLoS One 2: e553.
7. CURK, T., DEMSAR, J., XU, Q., LEBAN, G., PETROVIC, U., BRATKO, I., SHAUL-SKY, G. and ZUPAN, B. (2005). Microarray data mining with visual programming. Bioinformatics 21: 396-398.
8. DING, J., XU, H., FAIOLA, F., MA'AYAN, A. and WANG, J. (2012). Oct4 links multiple epigenetic pathways to the pluripotency network. Cell Res 22: 155-167.
9. DUTKOWSKI, J. and IDEKER, T. (2011). Protein networks as logic functions in development and cancer. PLoS Comput Biol 7: e1002180.
10. EDGAR, R., DOMRACHEV, M. and LASH, A.E. (2002). Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210.
11. HUANG, D.W., SHERMAN, B.T. and LEMPICKI, R.A. (2009a). Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37: 1-13.
12. HUANG, D.W., SHERMAN, B.T. and LEMPICKI, R.A. (2009b). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
13. JUNG, M., PETERSON, H., CHAVEZ, L., KAHLEM, P., LEHRACH, H., VILO, J. and ADJAYE, J. (2010). A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells. PLoS One 5: e10709.
14. KANEHISA, M., GOTO, S., SATO, Y., FURUMICHI, M. and TANABE, M. (2012). KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 40: D109-114.
15. KRALLINGER, M., VALENCIA, A. and HIRSCHMAN, L. (2008). Linking genes to literature: text mining, information extraction, and retrieval applications for biology. Genome Biol 9 Suppl 2: S8.
16. LICATA, L., BRIGANTI, L., PELUSO, D., PERFETTO, L., IANNUCCELLI, M., GA-LEOTA, E., SACCO, F., PALMA, A., NARDOZZA, A.P., SANTONICO, E. et al., (2012). MINT, the molecular interaction database: 2012 update. Nucleic Acids Res 40: D857-861.
17. LU, Z., KAO, H.Y., WEI, C.H., HUANG, M., LIU, J., KUO, C.J., HSU, C.N., TSAI, R.T., DAI, H.J., OKAZAKI, N. et al. (2011). The gene normalization task in BioCreative III. BMC Bioinformatics 12 Suppl 8: S2.
18. MAMO, S., CARTER, F., LONERGAN, P., LEAL, C.L., AL NAIB, A., MCGETTIGAN, P., MEHTA, J.P., EVANS, A.C. and FAIR, T. (2011). Sequential analysis of global gene expression profiles in immature and in vitro matured bovine oocytes: potential molecular markers of oocyte maturation. BMC Genomics 12: 151.
19. MATTHEWS, L., GOPINATH, G., GILLESPIE, M., CAUDY, M., CROFT, D., DE BONO, B., GARAPATI, P., HEMISH, J., HERMJAKOB, H., JASSAL, B. et al., (2009). Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 37: D619-622.
20. MULAS, F., ZAGAR, L., ZUPAN, B. and BELLAZZI, R. (2012). Supporting regenerative medicine by integrative dimensionality reduction. Methods Inf Med 51: 341-347.
21. MULLER, F.J., SCHULDT, B.M., WILLIAMS, R., MASON, D., ALTUN, G., PAPAPE-TROU, E.P., DANNER, S., GOLDMANN, J.E., HERBST, A., SCHMIDT, N.O. et al., (2011). A bioinformatic assay for pluripotency in human cells. Nat Methods 8: 315-317.
22. NIKITIN, A., EGOROV, S., DARASELIA, N. and MAZO, I. (2003). Pathway studio-the analysis and navigation of molecular networks. Bioinformatics 19: 2155-2157.
23. NITSCH, D., GONCALVES, J.P., OJEDA, F., DE MOOR, B. and MOREAU, Y. (2010). Candidate gene prioritization by network analysis of differential expression using machine learning approaches. BMC Bioinformatics 11: 460.
24. NUZZO, A., MULAS, F., GABETTA, M., ARBUSTINI, E., ZUPAN, B., LARIZZA, C. and BELLAZZI, R. (2010). Text Mining approaches for automated literature knowledge extraction and representation. Stud Health Technol Inform 160: 954-958.
25. PARDO, M., LANG, B., YU, L., PROSSER, H., BRADLEY, A., BABU, M.M. and CHOUDHARY, J. (2010). An expanded Oct4 interaction network: implications for stem cell biology, development, and disease. Cell Stem Cell 6: 382-395.
26. PARKINSON, H., KAPUSHESKY, M., KOLESNIKOV, N., RUSTICI, G., SHOJATALAB, M., ABEYGUNAWARDENA, N., BERUBE, H., DYLAG, M., EMAM, I., FARNE, A. et al., (2009). ArrayExpress update-from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res 37: D868-872.
27. PEDDINTI, D., MEMILI, E. and BURGESS, S.C. (2010). Proteomics-based systems biology modeling of bovine germinal vesicle stage oocyte and cumulus cell interaction. PLoS One 5: e11240.
28. SUBRAMANIAN, A., TAMAYO, P., MOOTHA, V.K., MUKHERJEE, S., EBERT, B.L., GILLETTE, M.A., PAULOVICH, A., POMEROY, S.L., GOLUB, T.R., LANDER, E.S. et al., (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102: 15545-15550.
29. SZKLARCZYK, D., FRANCESCHINI, A., KUHN, M., SIMONOVIC, M., ROTH, A., MINGUEZ, P., DOERKS, T., STARK, M., MULLER, J., BORK, P. et al., (2011). The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 39: D561-568.
30. THOMAS, P.D., CAMPBELL, M.J., KEJARIWAL, A., MI, H., KARLAK, B., DAVERMAN, R., DIEMER, K., MURUGANUJAN, A. and NARECHANIA, A. (2003). PANTHER: a library of protein families and subfamilies indexed by function. Genome Res 13: 2129-2141.
31. WEEBER, M., KORS, J.A. and MONS, B. (2005). Online tools to support literaturebased discovery in the life sciences. Brief Bioinform 6: 277-286.
32. ZAGAR, L., MULAS, F., GARAGNA, S., ZUCCOTTI, M., BELLAZZI, R. and ZUPAN, B. (2011). Stage prediction of embryonic stem cell differentiation from genomewide expression data. Bioinformatics 27: 2546-2553.
33. ZHANG, P., NI, X., GUO, Y., GUO, X., WANG, Y., ZHOU, Z., HUO, R. and SHA, J. (2009). Proteomic-based identification of maternal proteins in mature mouse oocytes. BMC Genomics 10: 348.
34. ZUCCOTTI, M., MERICO, V., BELLONE, M., MULAS, F., SACCHI, L., REBUZZINI, P., PRIGIONE, A., REDI, C.A., BELLAZZI, R., ADJAYE, J. et al., (2011). Gatekeeper of pluripotency: a common Oct4 transcriptional network operates in mouse eggs and embryonic stem cells. BMC Genomics 12: 1-13.
35. ZUCCOTTI, M., MERICO, V., SACCHI, L., BELLONE, M., BRINK, T.C., BELLAZZI, R., STEFANELLI, M., REDI, C.A., GARAGNA, S. and ADJAYE, J. (2008). Maternal Oct-4 is a potential key regulator of the developmental competence of mouse oocytes. BMC Dev Biol 8: 97.