SpermatogenesisOnline 1.0: A resource for spermatogenesis based on manual literature curation and genome-wide data mining

Nucleic Acids Research

Volumn 41, Issue D1, 2013, Pages

  Zhang, Yuanwei ^a   Zhong, Liangwen ^a   Xu, Bo ^a,f   Yang, Yifan ^b   Ban, Rongjun ^c   Zhu, Jun ^d   Cooke, Howard J ^a,e   Hao, QiaoMei ^a   Shi, Qinghua ^a  

^a UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^b UNIVERSITY OF KENTUCKY   (United States)

^c NANJING UNIVERSITY   (China)

^d NATIONAL UNIVERSITY OF DEFENSE TECHNOLOGY   (China)

^e UNIVERSITY OF EDINBURGH   (United Kingdom)

^f ANHUI MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOINFORMATICS; COMPUTER INTERFACE; DATA MINING; FACTUAL DATABASE; GENETIC ALGORITHM; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GREED AUC STEPWISE MODEL; HUMAN GENOME; INFORMATION RETRIEVAL; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROBABILITY; PROTEIN PROTEIN INTERACTION; RELIABILITY; SPERMATOGENESIS; SPERMATOGENESISONLINE 1.0;

ANIMALS; CATTLE; DATA MINING; DATABASES, GENETIC; GENOMICS; HUMANS; INTERNET; MALE; MICE; MOLECULAR SEQUENCE ANNOTATION; RATS; SPERMATOGENESIS; TRANSCRIPTOME; USER-COMPUTER INTERFACE;

MUS MUSCULUS;

EID: 84876586731     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1186     Document Type: Article

References (35)

1. Cooke, H.J. and Saunders, P.T. (2002) Mouse models of male infertility. Nat. Rev. Genet., 3, 790-801.
2. Guan, K., Nayernia, K., Maier, L.S., Wagner, S., Dressel, R., Lee, J.H., Nolte, J., Wolf, F., Li, M., Engel, W. et al. (2006) Pluripotency of spermatogonial stem cells from adult mouse testis. Nature, 440, 1199-1203.
3. Clermont, Y., Oko, R. and Hermo, L. (1993) Cell biology of mammalian spermiogenesis. Cell and Molecular Biology of the Testis., 332-376. Desjardins C, Ewing L (eds), Oxford University Press.
4. Holstein, A.F., Schulze, W. and Davidoff, M. (2003) Understanding spermatogenesis is a prerequisite for treatment. Reprod. Biol. Endocrinol., 1, 107.
5. Brinster, R.L. and Zimmermann, J.W. (1994) Spermatogenesis following male germ-cell transplantation. Proc. Natl Acad. Sci. USA, 91, 11298-11302.
6. Oatley, J.M. and Brinster, R.L. (2008) Regulation of spermatogonial stem cell self-renewal in mammals. Annu. Rev. Cell Dev. Biol., 24, 263-286.
7. Fuchs, E., Tumbar, T. and Guasch, G. (2004) Socializing with the neighbors: stem cells and their niche. Cell, 116, 769-778.
8. de Rooij, D.G. and Russell, L.D. (2000) All you wanted to know about spermatogonia but were afraid to ask. J. Androl., 21, 776-798.
9. Page, S.L. and Hawley, R.S. (2004) The genetics and molecular biology of the synaptonemal complex. Annu. Rev. Cell Dev. Biol., 20, 525-558.
10. Ward, W.S. and Coffey, D.S. (1991) DNA packaging and organization in mammalian spermatozoa: comparison with somatic cells. Biol. Reprod., 44, 569-574.
11. Russell, L.D. (1990) Histological and histopathological evaluation of the testis., 119-161. Ettlin R, Sinha-Hikim AP, Clegg ED, (Eds), Cache River Press. May 16 (doi:10.1111/j.1365-2605.1993 .tb01156.x; epub ahead of print).
12. Ge, R.S. and Hardy, M.P. (1998) Variation in the end products of androgen biosynthesis and metabolism during postnatal differentiation of rat Leydig cells. Endocrinology, 139, 3787-3795.
13. Liu, Y., Yao, Z.X. and Papadopoulos, V. (2005) Cytochrome P450 17alpha hydroxylase/17,20 lyase (CYP17) function in cholesterol biosynthesis: identification of squalene monooxygenase (epoxidase) activity associated with CYP17 in Leydig cells. Mol. Endocrinol., 19, 1918-1931.
14. Amlani, S. and Vogl, A.W. (1988) Changes in the distribution of microtubules and intermediate filaments in mammalian Sertoli cells during spermatogenesis. Anat. Rec., 220, 143-160.
15. Matzuk, M.M. and Lamb, D.J. (2008) The biology of infertility: research advances and clinical challenges. Nat. Med., 14, 1197-1213.
16. 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-D872.
17. Keshava Prasad, T.S., Goel, R., Kandasamy, K., Keerthikumar, S., Kumar, S., Mathivanan, S., Telikicherla, D., Raju, R., Shafreen, B., Venugopal, A. et al. (2009) Human Protein Reference Database - 2009 update. Nucleic Acids Res., 37, D767-D772.
18. Stark, C., Breitkreutz, B.J., Chatr-Aryamontri, A., Boucher, L., Oughtred, R., Livstone, M.S., Nixon, J., Van Auken, K., Wang, X., Shi, X. et al. (2011) The BioGRID Interaction Database: 2011 update. Nucleic Acids Res., 39, D698-D704.
19. Xenarios, I., Salwinski, L., Duan, X.J., Higney, P., Kim, S.M. and Eisenberg, D. (2002) DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res., 30, 303-305.
20. Licata, L., Briganti, L., Peluso, D., Perfetto, L., Iannuccelli, M., Galeota, 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-D861.
21. Kerrien, S., Aranda, B., Breuza, L., Bridge, A., Broackes-Carter, F., Chen, C., Duesbury, M., Dumousseau, M., Feuermann, M., Hinz, U. et al. (2012) The IntAct molecular interaction database in 2012. Nucleic Acids Res., 40, D841-D846.
22. 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-D568.
23. Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K. and Madden, T.L. (2009) BLAST+: architecture and applications. BMC Bioinformatics, 10, 421.
24. Mi, H., Dong, Q., Muruganujan, A., Gaudet, P., Lewis, S. and Thomas, P.D. (2010) PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res., 38, D204-D210.
25. Ostlund, G., Schmitt, T., Forslund, K., Kostler, T., Messina, D.N., Roopra, S., Frings, O. and Sonnhammer, E.L. (2010) InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res., 38, D196-D203.
26. Lardenois, A., Gattiker, A., Collin, O., Chalmel, F. and Primig, M. (2010) GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle. Database, 2010, baq030.
27. Hsueh, A.J. and Rauch, R. (2012) Ovarian Kaleidoscope database: ten years and beyond. Biol. Reprod., 86, 192.
28. Saunders, P.T., Turner, J.M., Ruggiu, M., Taggart, M., Burgoyne, P.S., Elliott, D. and Cooke, H.J. (2003) Absence of mDazl produces a final block on germ cell development at meiosis. Reproduction, 126, 589-597.
29. Tanaka, S.S., Toyooka, Y., Akasu, R., Katoh-Fukui, Y., Nakahara, Y., Suzuki, R., Yokoyama, M. and Noce, T. (2000) The mouse homolog of Drosophila Vasa is required for the development of male germ cells. Genes Dev., 14, 841-853.
30. Reuter, M., Chuma, S., Tanaka, T., Franz, T., Stark, A. and Pillai, R.S. (2009) Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA profile. Nat. Struct. Mol. Biol., 16, 639-646.
31. Sada, A., Suzuki, A., Suzuki, H. and Saga, Y. (2009) The RNA-binding protein NANOS2 is required to maintain murine spermatogonial stem cells. Science, 325, 1394-1398.
32. Schlesser, H.N., Simon, L., Hofmann, M.C., Murphy, K.M., Murphy, T., Hess, R.A. and Cooke, P.S. (2008) Effects of ETV5 (ets variant gene 5) on testis and body growth, time course of spermatogonial stem cell loss, and fertility in mice. Biol. Reprod., 78, 483-489.
33. Hao, J., Yamamoto, M., Richardson, T.E., Chapman, K.M., Denard, B.S., Hammer, R.E., Zhao, G.Q. and Hamra, F.K. (2008) Sohlh2 knockout mice are male-sterile because of degeneration of differentiating type A spermatogonia. Stem Cells, 26, 1587-1597.
34. Oatley, J.M., Kaucher, A.V., Avarbock, M.R. and Brinster, R.L. (2010) Regulation of mouse spermatogonial stem cell differentiation by STAT3 signaling. Biol. Reprod., 83, 427-433.
35. Barbosa-Silva, A., Fontaine, J.F., Donnard, E.R., Stussi, F., Ortega, J.M. and Andrade-Navarro, M.A. (2011) PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. BMC Bioinformatics, 12, 435.