$\require{mediawiki-texvc}$

연합인증

연합인증 가입 기관의 연구자들은 소속기관의 인증정보(ID와 암호)를 이용해 다른 대학, 연구기관, 서비스 공급자의 다양한 온라인 자원과 연구 데이터를 이용할 수 있습니다.

이는 여행자가 자국에서 발행 받은 여권으로 세계 각국을 자유롭게 여행할 수 있는 것과 같습니다.

연합인증으로 이용이 가능한 서비스는 NTIS, DataON, Edison, Kafe, Webinar 등이 있습니다.

한번의 인증절차만으로 연합인증 가입 서비스에 추가 로그인 없이 이용이 가능합니다.

다만, 연합인증을 위해서는 최초 1회만 인증 절차가 필요합니다. (회원이 아닐 경우 회원 가입이 필요합니다.)

연합인증 절차는 다음과 같습니다.

최초이용시에는
ScienceON에 로그인 → 연합인증 서비스 접속 → 로그인 (본인 확인 또는 회원가입) → 서비스 이용

그 이후에는
ScienceON 로그인 → 연합인증 서비스 접속 → 서비스 이용

연합인증을 활용하시면 KISTI가 제공하는 다양한 서비스를 편리하게 이용하실 수 있습니다.

In silico Discovery of Genes Expressed in Liver, Kidney, Spleen and Small Intestine of Pigs

Asian-Australasian journal of animal sciences, v.18 no.2, 2005년, pp.170 - 178  

Pan, Zengxiang (College of Animal Science and Technology, Nanjing Agricultural University) ,  Liu, Honglin (College of Animal Science and Technology, Nanjing Agricultural University) ,  Chen, Jie (College of Animal Science and Technology, Nanjing Agricultural University) ,  Xu, Dan (College of Animal Science and Technology, Nanjing Agricultural University) ,  Jiang, Zhihua (Department of Animal Sciences, Washington State University) ,  Xie, Zhuang (College of Animal Science and Technology, Nanjing Agricultural University)

Abstract AI-Helper 아이콘AI-Helper

An in silico approach was developed to survey the genes expressed in four internal organs of pig: liver, kidney, spleen and small intestine. The major procedures of the approach included: (1) BLAST searching against GenBank "est_others" database using human cDNA sequences as queries to screen the po...

주제어

AI 본문요약
AI-Helper 아이콘 AI-Helper

* AI 자동 식별 결과로 적합하지 않은 문장이 있을 수 있으니, 이용에 유의하시기 바랍니다.

제안 방법

  • (1) counting the human genes and their homologous porcine ESTs expressed in the liver, kidney, spleen, and small intestine according to the human chromosome number, and identifying the extremely significant match records in the respective tissues (represented by the top 10).
  • In this study, we built up an in silica approach to identify the homologies between cDNA sequences of human genes and porcine ESTs sequences by utilizing the present software tools and developing Java programs. First, a standalone BLAST searching program was installed and used to perform BLAST searches to annotate porcine ESTs expressed in the major internal organs. The major procedures included firstly: (1) BLAST searching against GenBank “est_others” database using human cDNA sequences as queries, (2) identifying and screening the porcine orthologous ESTs, (3) classifying the porcine ESTs records by resources according to certain criteria, (4) collecting and arranging data for ESTs specifically expressed in the major internal organs.
  • Realizing these, we developed an in silico study here. In this study, retrieving homologous sequences between human genes and porcine ESTs sequences by BLAST, allowed us to annotate the porcine ESTs derived from the major internal organs by a fresh gene oriented approach which characterized genes expressed in some tissues from genes to ESTs. This approach provided tools and information for rapid discovery of genes of interest.
  • In this study, we built up an in silica approach to identify the homologies between cDNA sequences of human genes and porcine ESTs sequences by utilizing the present software tools and developing Java programs. First, a standalone BLAST searching program was installed and used to perform BLAST searches to annotate porcine ESTs expressed in the major internal organs.
  • The major procedures included firstly: (1) BLAST searching against GenBank “est_others” database using human cDNA sequences as queries, (2) identifying and screening the porcine orthologous ESTs, (3) classifying the porcine ESTs records by resources according to certain criteria, (4) collecting and arranging data for ESTs specifically expressed in the major internal organs. Secondly, four Java programs were developed for sequences collection, sequences alignment and data processing, which included: (1) Web robot, used for collecting mRNA accession numbers by detecting all human chromosome information web pages, (2) Light query, used for automatically querying the NCBI search engine (http://wwww.ncbi.nlm.nih.gov/entrez/) for the FASTA sequences using mRNA accession numbers as search fields, (3) BlastFilter, used to filter out the BLAST matches that do not represent the porcine ESTs or do not meet the requirements with sequence identity by higher than 80% within a continuous alignment of sequences longer than 100 bp, (4) Parser/Screen, used to process Plain text in BLAST research result pages so as to analyze more conveniently and easily, and ultimately form the Microsoft Excel format tables.
  • Secondly, four Java programs were developed for sequences collection, sequences alignment and data processing, which included: (1) Web robot, used for collecting mRNA accession numbers by detecting all human chromosome information web pages, (2) Light query, used for automatically querying the NCBI search engine (http://wwww.ncbi.nlm.nih.gov/entrez/) for the FASTA sequences using mRNA accession numbers as search fields, (3) BlastFilter, used to filter out the BLAST matches that do not represent the porcine ESTs or do not meet the requirements with sequence identity by higher than 80% within a continuous alignment of sequences longer than 100 bp, (4) Parser/Screen, used to process Plain text in BLAST research result pages so as to analyze more conveniently and easily, and ultimately form the Microsoft Excel format tables.
  • So for database miners or users, there are three challenges to confront: (1) making full and efficient use of the present software tools resources on-line or off-line in sequence analysis, genetic analysis, and data processing etc. (2) developing a certain program for large-scale in silico study, e.g., four programs 'Web robot’, 'Light query’, 'BlastFilter’, and 'Parser/Screen’ were developed by Java in this study.
  • To detect the gene expression profiles in the major internal organs of the pig, we have developed an in silico approach for mining the NCBI (The National Center for Biotechnology Information) porcine EST sequence resources using the human genome cDNA sequences as references. The information reported in this paper should be useful for researchers in the field to analyze genes and proteins of their own interest, and to study comparative and functional genomics.
  • The major procedures included firstly: (1) BLAST searching against GenBank “est_others” database using human cDNA sequences as queries, (2) identifying and screening the porcine orthologous ESTs, (3) classifying the porcine ESTs records by resources according to certain criteria, (4) collecting and arranging data for ESTs specifically expressed in the major internal organs.
  • First, a standalone BLAST searching program was installed and used to perform BLAST searches to annotate porcine ESTs expressed in the major internal organs. The major procedures included firstly: (1) BLAST searching against GenBank “est_others” database using human cDNA sequences as queries, (2) identifying and screening the porcine orthologous ESTs, (3) classifying the porcine ESTs records by resources according to certain criteria, (4) collecting and arranging data for ESTs specifically expressed in the major internal organs. Secondly, four Java programs were developed for sequences collection, sequences alignment and data processing, which included: (1) Web robot, used for collecting mRNA accession numbers by detecting all human chromosome information web pages, (2) Light query, used for automatically querying the NCBI search engine (http://wwww.
본문요약 정보가 도움이 되었나요?

참고문헌 (46)

  1. Adams, M. D., J. M. Kelley, J. D. Gocayne, M. Dubnick, M. H. Polymeropoulos, H. Xiao, C. R. Merril, A. Wu, B. Olde and R. F. Moreno. 1991. Complementary DNA sequencing: expressed sequence tags and human genome project. Sci. 252:1651-1656 

  2. Attwood, T. K. and C. J. Miller. 2002. Progress in bioinformatics and the importance of being earnest. Biotechnol. Annu. Rev. 8:1-54 

  3. Austen, B., O. el-Agnaf, S. Nagala, B. Patel, N. Gunasekera, M. Lee and V. Lelyveld. 2002. Properties of neurotoxic peptides related to the BRI gene. Biochem. Soc. Trans. 30:557-559 

  4. Balas, A., S. Santos, M. J. Aviles, F. Garcia-Sanchez, R. Lillo and J. L. Vicario. 2000. Identification by sequencing based typing and complete coding region analysis of three new HLA class II alleles: DRB3 ${\times}$ 0210, DRB3×0211 and DQB1 ${\times}$ 0310. Tissue Antigens. 56:380-384 

  5. Barnes, M. R. 2002. Psychiatric genetics in silico: databases and tools for psychiatric geneticists. Psychiatric Genetics 12:67-73 

  6. Bedford, M. T., R. Reed and P. Leder. 1998. WW domainmediated interactions reveal a spliceosome-associated protein that binds a third class of proline-rich motif: the proline glycine and methionine-rich motif. Proc. Natl. Acad. Sci. USA 95:10602-10607 

  7. Birney, E., M. Clamp and T. Hubbard. 2002. Databases and tools for browsing genomes. Annu. Rev. Genomics Hum. Genet. 3:293-310 

  8. Buddhikot, M., E. Falkenstein, M. Wehling and S. Meizel. 1999. Recognition of a human sperm surface protein involved in the progesterone-initiated acrosome reaction by antisera against an endomembrane progesterone binding protein from porcine liver. Molecular and Cellular Endocrinology 158:187-193 

  9. Campeau, E., L. R. Desviat, D. Leclerc, X. Wu, B. Perez, M. Ugarte and R. A. Gravel. 2001. Structure of the PCCA gene and distribution of mutations causing propionic academia. Mol. Genet. Metab. 74:238-247 

  10. Chalasani, N., J. C. Gorski, M. S. Asghar, R. A. Asgha, B. Foresman, S. D. Hall and D. W. Crabb. 2003. Hepatic cytochrome P450 2E1 activity in nondiabetic patients with nonalcoholic steatohepatitis. Hepatology 37:544-550 

  11. Dearden, P. and M. Akam. 2000. Computational biology: Segmentation in silico. Nature 406:131-132 

  12. Dumont, P., J. I. Leu, A. C. Della Pietra 3rd, D. L. George and M. Murphy. 2003. The codon 72 polymorphic variants of p53 have markedly different apoptotic potential. Nat. Genet. 33:357-365 

  13. Esposito, G., L. Vitagliano, R. Santamaria, A. Viola, A. Zagari and F. Salvatore. 2002. Structural and functional analysis of aldolase B mutants related to hereditary fructose intolerance. FEBS Lett. 531:152-156 

  14. Farber, C. R. and J. F. Medrano. 2003. Putative in silico mapping of DNA sequences to livestock genome maps using SSLP flanking sequences. Animal Genetics 34:11-18 

  15. Gerdes, D., M. Wehling, B. Leube and E. Falkenstein. 1998. Cloning and tissue expression of two putative steroid membrane receptors. Biol. Chem. 379:907-911 

  16. Gill, R. W. and P. Sanseau. 2000. Rapid in silico cloning of genes using expressed sequence tags (ESTs). Biotechnol. Ann. Rev. 5:25-44 

  17. Gorinstein, S., A. Caspi, A. Rosen, I. Goshev, M. Zemser, M. Weisz, M. C. Anon, I. Libman, H. T. Lerner and S. Trakhtenberg. 2002. Structure characterization of human serum proteins in solution and dry state. J. Pept. Res. 59:71-78 

  18. Guimaraes, D. P. and P. Hainaut. 2002. TP53: a key gene in human cancer. Biochimie. 84:83-93 

  19. Heaton, J. H., W. M. Dlakic, M. Dlakic and T. D. Gelehrter. 2001. Identification and cDNA cloning of a novel RNA-binding protein that interacts with the cyclic nucleotide-responsive sequence in the Type-1 plasminogen activator inhibitor mRNA. J. Biol. Chem. 276:3341-3347 

  20. Ishii, J., H. Adachi, J. Aoki, H. Koizumi, S. Tomita, T. Suzuki, M. Tsujimoto, K. Inoue and H. Arai. 2002. SREC-II, a new member of the scavenger receptor type F family, trans-interacts with SREC-I through its extracellular domain. J. Biol. Chem. 277:39696-39702 

  21. Jiang, Z., M. Zhang, V. D. Wasem, J. J. Michal, H. Zhang and R. W. Wright, Jr. 2003. Census of Genes Expressed in Porcine Embryos and Reproductive Tissues by Mining EST Database Based on the Human Genes. Biol. Reprod. 69:1177-1182 

  22. Lee, J. H., C. Moran1 and C. S. Park. 2003. Current Status of Comparative Mapping in Livestock. Asian-Aust. J. Anim. Sci. 16:1411-1420 

  23. Lejus, C., A. Fautrel, Y. Malledant and A. Guillouzo. 2002. Inhibition of the cytochrome P450 2E1 by propofol in human and porcine liver microsomes. Biochemical pharmacology. 64:1151-1156 

  24. Lynn, D. J., A. T. Lloyd and C. O'Farrelly. 2003. Bioinformatics: implications for medical research and clinical practice. Clin. Invest. Med. 26:70-74 

  25. Martin, K. J. and A. B. Pardee. 2000. Identifying expressed genes. PNAS. 97:3789-3791 

  26. Meijssen, S., H. van Dijk, C. Verseyden, D. W. Erkelens and M. C. Cabezas. 2002. Delayed and exaggerated postprandial complement component 3 response in familial combined hyperlipidemia. Arterioscler. Thromb. Vasc. Biol. 22:811-816 

  27. Moriyama, K. and I. Yahara. 2002. Human CAP1 is a key factor in the recycling of cofilin and actin for rapid actin turnover. J. Cell. Sci. 115:1591-1601 

  28. Mostert, V. 2000. Selenoprotein P: properties, functions, and regulation. Arch. Biochem. Biophys. 376:433-438 

  29. Narayanan, B. A., N. K. Narayanan, G. G. Re and D. W. Nixon. 2003. Differential expression of genes induced by resveratrol in LNCaP cells: P53-mediated molecular targets. Int. J. Cancer. 104:204-212 

  30. Nieto, N., S. L. Friedman and A. I. Cederbaum. 2002. Cytochrome P450 2E1-derived reactive oxygen species mediate paracrine stimulation of collagen I protein synthesis by hepatic stellate cells. J. Biol. Chem. 277:9853-9864 

  31. Pandey, A. and F. Lewitter. 1999. Nucleotide sequence databases: a gold mine for biologists. Trends Biochem. Sci. 24:276-280 

  32. Pertea, G., X. Huang, F. Liang, V. Antonescu, R. Sultana, S. Karamycheva, Y. Lee, J. White, F. Cheung, B. Parvizi, J. Tsai and J. Quackenbush. 2003. Bioinformatics 19:651-652 

  33. Pittois, K., W. Deleersnijder and J. Merregaert. 1998. cDNA sequence analysis, chromosomal assignment and expression pattern of the gene coding for integral membrane protein 2B. Gene. 217:141-149 

  34. Pruess, M., W. Fleischmann, A. Kanapin, Y. Karavidopoulou, P. Kersey, E. Kriventseva, V. Mittard, N. Mulder, I. Phan, F. Servant and R. Apweiler. 2003. The Proteome Analysis database: a tool for the in silico analysis of whole proteomes. Nucleic Acids Res. 31:414-417 

  35. Rasmussen, T. N., P. Schmidt, S. S. Poulsen and J. J. Holst. 2001a. Localisation and neural control of the release of calcitonin gene-related peptide (CGRP) from the isolated perfused porcine ileum. Regulatory Peptides. 98:137-143 

  36. Rasmussen, T. N., P. Schmidt, S. S. Poulsen and J. J. Holst. 2001b. Effect of calcitonin gene-related peptide (CGRP) on motility and on the release of substance P, neurokinin A, somatostatin and gastrin in the isolated perfused porcine antrum. Neurogastroenterol. Mot. 13:353-359 

  37. Rodriguez-Pombo, P., C. Perez-Cerda, L. R. Desviat, B. Perez and M. Ugarte. 2002. Transfection Screening for Defects in the PCCA and PCCB Genes Encoding Propionyl-CoA Carboxylase Subunits. Mol. Genet. Metab. 75:276-279 

  38. Rohrer, G. A., S. C. Fahrenkrug, D. Nonneman, N. Tao and W. C. Warren. 2002. Mapping microsatellite markers identified in porcine EST sequences. Animal Genetics 33:372-376 

  39. Saito, Y. and K. Takahashi. 2002. Characterization of selenoprotein P as a selenium supply protein. Eur. J. Biochem. 269:5746-5751 

  40. Scarr, R. B. 2002. PDCD2 is a negative regulator of HCF1 (C1). Oncogene. 21:5245-5254 

  41. Shito, M., N. H. Kim, H. Baskaran, A. W. Tilles, R. G. Tompkins, M. L. Yarmush and M. Toner. 2001. In vitro and in vivo evaluation of the Albumin synthesis rate of porcine hepatocytes in a flat-plate bioreactor. Artificial Organs. 25:571-578 

  42. Skrabanek, L. and F. Campagne. 2001. Tissueinfo: highthroughput identification of tissues expression profiles and specificity. Nucleic Acids Res. 29:21-102 

  43. Strausberg, R. L., E. A. Feingold, R. D. Klausner and F. S. Collins. 1999. The Mammalian Gene Collection. Science 286:455-457 

  44. Tolan, D. R. and E. E. Penhoet. 1986. Characterization of the human aldolase B gene. Mol. Biol. Med. 3:245-264 

  45. Wimmers, K., S. Mekchay, S. Ponsuksili, T. Hardge, M. Yerle and K. Schellander. 2001. Polymorphic sites in exon 15 and 30 of the porcine C3 gene. Animal Genetics 32:40-53 

  46. Yamada, Y., T. Doi, T. Hamakubo and T. Kodama. 1998. Scavenger receptor family proteins: roles for atherosclerosis, host defence and disorders of the central nervous system. Cell Mol. Life Sci. 54:628-640 

저자의 다른 논문 :

관련 콘텐츠

오픈액세스(OA) 유형

BRONZE

출판사/학술단체 등이 한시적으로 특별한 프로모션 또는 일정기간 경과 후 접근을 허용하여, 출판사/학술단체 등의 사이트에서 이용 가능한 논문

섹션별 컨텐츠 바로가기

AI-Helper ※ AI-Helper는 오픈소스 모델을 사용합니다.

AI-Helper 아이콘
AI-Helper
안녕하세요, AI-Helper입니다. 좌측 "선택된 텍스트"에서 텍스트를 선택하여 요약, 번역, 용어설명을 실행하세요.
※ AI-Helper는 부적절한 답변을 할 수 있습니다.

선택된 텍스트