Literature DB >> 12213203

Computational analysis of alternative splicing using EST tissue information.

Hanqing Xie1, Wei-yong Zhu, Alon Wasserman, Vladimir Grebinskiy, Andrew Olson, Liat Mintz.   

Abstract

Expressed sequence tags (ESTs) from normal and tumor tissues have been deposited in public databases. These ESTs and all mRNA sequences were aligned with the human genome sequence using LEADS, Compugen's alternative splicing modeling platform. We developed a novel computational approach to analyze tissue information of aligned ESTs in order to identify cancer-specific alternative splicing and gene segments highly expressed in particular cancers. Several genes, including one encoding a possible pre-mRNA splicing factor, displayed cancer-specific alternative splicing. In addition, multiple candidate gene segments highly expressed in colon cancers were identified.

Entities:  

Mesh：

Year:  2002        PMID： 12213203     DOI： 10.1006/geno.2002.6841

Source DB:  PubMed          Journal:  Genomics        ISSN： 0888-7543            Impact factor:   5.736


  13 in total

1.  A transcript finishing initiative for closing gaps in the human transcriptome.

Authors:  Mari Cleide Sogayar; Anamaria A Camargo; Fabiana Bettoni; Dirce Maria Carraro; Lilian C Pires; Raphael B Parmigiani; Elisa N Ferreira; Eloísa de Sá Moreira; Maria do Rosário D de O Latorre; Andrew J G Simpson; Luciana Oliveira Cruz; Theri Leica Degaki; Fernanda Festa; Katlin B Massirer; Mari C Sogayar; Fernando Camargo Filho; Luiz Paulo Camargo; Marco A V Cunha; Sandro J De Souza; Milton Faria; Silvana Giuliatti; Leonardo Kopp; Paulo S L de Oliveira; Paulo B Paiva; Anderson A Pereira; Daniel G Pinheiro; Renato D Puga; Jorge Estefano S de Souza; Dulcineia M Albuquerque; Luís E C Andrade; Gilson S Baia; Marcelo R S Briones; Ana M S Cavaleiro-Luna; Janete M Cerutti; Fernando F Costa; Eugenia Costanzi-Strauss; Enilza M Espreafico; Adriana C Ferrasi; Emer S Ferro; Maria A H Z Fortes; Joelma R F Furchi; Daniel Giannella-Neto; Gustavo H Goldman; Maria H S Goldman; Arthur Gruber; Gustavo S Guimarães; Christine Hackel; Flavio Henrique-Silva; Edna T Kimura; Suzana G Leoni; Cláudia Macedo; Bettina Malnic; Carina V Manzini B; Suely K N Marie; Nilce M Martinez-Rossi; Marcelo Menossi; Elisabete C Miracca; Maria A Nagai; Francisco G Nobrega; Marina P Nobrega; Sueli M Oba-Shinjo; Márika K Oliveira; Guilherme M Orabona; Audrey Y Otsuka; Maria L Paço-Larson; Beatriz M C Paixão; Jose R C Pandolfi; Maria I M C Pardini; Maria R Passos Bueno; Geraldo A S Passos; Joao B Pesquero; Juliana G Pessoa; Paula Rahal; Cláudia A Rainho; Caroline P Reis; Tatiana I Ricca; Vanderlei Rodrigues; Silvia R Rogatto; Camila M Romano; Janaína G Romeiro; Antonio Rossi; Renata G Sá; Magaly M Sales; Simone C Sant'Anna; Patrícia L Santarosa; Fernando Segato; Wilson A Silva; Ismael D C G Silva; Neusa P Silva; Andrea Soares-Costa; Maria F Sonati; Bryan E Strauss; Eloiza H Tajara; Sandro R Valentini; Fabiola E Villanova; Laura S Ward; Dalila L Zanette
Journal:  Genome Res       Date:  2004-06-14       Impact factor: 9.043

2.  Characteristics and regulatory elements defining constitutive splicing and different modes of alternative splicing in human and mouse.

Authors:  Christina L Zheng; Xiang-Dong Fu; Michael Gribskov
Journal:  RNA       Date:  2005-10-26       Impact factor: 4.942

3.  Mammalian mRNA splice-isoform selection is tightly controlled.

Authors:  Jennifer L Chisa; David T Burke
Journal:  Genetics       Date:  2006-12-18       Impact factor: 4.562

4.  Transcriptome analysis of human gastric cancer.

Authors:  Jung-Hwa Oh; Jin Ok Yang; Yoonsoo Hahn; Mi-Rang Kim; Sang-Soon Byun; Yeo-Jin Jeon; Jeong-Min Kim; Kyu-Sang Song; Seung-Moo Noh; Sangsoo Kim; Hyang-Sook Yoo; Yong Sung Kim; Nam-Soon Kim
Journal:  Mamm Genome       Date:  2005-12-08       Impact factor: 2.957

5.  SpliceTrap: a method to quantify alternative splicing under single cellular conditions.

Authors:  Jie Wu; Martin Akerman; Shuying Sun; W Richard McCombie; Adrian R Krainer; Michael Q Zhang
Journal:  Bioinformatics       Date:  2011-09-06       Impact factor: 6.937

6.  Metabolism of soluble sugars in developing melon fruit: a global transcriptional view of the metabolic transition to sucrose accumulation.

Authors:  Nir Dai; Shahar Cohen; Vitaly Portnoy; Galil Tzuri; Rotem Harel-Beja; Maya Pompan-Lotan; Nir Carmi; Genfa Zhang; Alex Diber; Sarah Pollock; Hagai Karchi; Yelena Yeselson; Marina Petreikov; Shmuel Shen; Uzi Sahar; Ran Hovav; Efraim Lewinsohn; Yakov Tadmor; David Granot; Ron Ophir; Amir Sherman; Zhangjun Fei; Jim Giovannoni; Yosef Burger; Nurit Katzir; Arthur A Schaffer
Journal:  Plant Mol Biol       Date:  2011-03-09       Impact factor: 4.076

7.  The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags.

Authors:  Helena Brentani; Otávia L Caballero; Anamaria A Camargo; Aline M da Silva; Wilson Araújo da Silva; Emmanuel Dias Neto; Marco Grivet; Arthur Gruber; Pedro Edson Moreira Guimaraes; Winston Hide; Christian Iseli; C Victor Jongeneel; Janet Kelso; Maria Aparecida Nagai; Elida Paula Benquique Ojopi; Elisson C Osorio; Eduardo M R Reis; Gregory J Riggins; Andrew John George Simpson; Sandro de Souza; Brian J Stevenson; Robert L Strausberg; Eloiza H Tajara; Sergio Verjovski-Almeida; Marcio Luis Acencio; Mário Henrique Bengtson; Fabiana Bettoni; Walter F Bodmer; Marcelo R S Briones; Luiz Paulo Camargo; Webster Cavenee; Janete M Cerutti; Luis Eduardo Coelho Andrade; Paulo César Costa dos Santos; Maria Cristina Ramos Costa; Israel Tojal da Silva; Marcos Roberto H Estécio; Karine Sa Ferreira; Frank B Furnari; Milton Faria; Pedro A F Galante; Gustavo S Guimaraes; Adriano Jesus Holanda; Edna Teruko Kimura; Maarten R Leerkes; Xin Lu; Rui M B Maciel; Elizabeth A L Martins; Katlin Brauer Massirer; Analy S A Melo; Carlos Alberto Mestriner; Elisabete Cristina Miracca; Leandro Lorenco Miranda; Francisco G Nobrega; Paulo S Oliveira; Apua C M Paquola; José Rodrigo C Pandolfi; Maria Ines de Moura Campos Pardini; Fabio Passetti; John Quackenbush; Beatriz Schnabel; Mari Cleide Sogayar; Jorge E Souza; Sandro R Valentini; Andre C Zaiats; Elisabete Jorge Amaral; Liliane A T Arnaldi; Amelia Goes de Araújo; Simone Aparecida de Bessa; David C Bicknell; Maria Eugenia Ribeiro de Camaro; Dirce Maria Carraro; Helaine Carrer; Alex F Carvalho; Christian Colin; Fernando Costa; Cyntia Curcio; Ismael Dale Cotrim Guerreiro da Silva; Neusa Pereira da Silva; Márcia Dellamano; Hamza El-Dorry; Enilza Maria Espreafico; Ari José Scattone Ferreira; Cristiane Ayres Ferreira; Maria Angela H Z Fortes; Angelita Habr Gama; Daniel Giannella-Neto; Maria Lúcia C C Giannella; Ricardo R Giorgi; Gustavo Henrique Goldman; Maria Helena S Goldman; Christine Hackel; Paulo Lee Ho; Elza Myiuki Kimura; Luiz Paulo Kowalski; Jose E Krieger; Luciana C C Leite; Ademar Lopes; Ana Mercedes S C Luna; Alan Mackay; Suely Kazue Nagahashi Mari; Adriana Aparecida Marques; Waleska K Martins; André Montagnini; Mario Mourão Neto; Ana Lucia T O Nascimento; A Munro Neville; Marina P Nobrega; Mike J O'Hare; Audrey Yumi Otsuka; Anna Izabel Ruas de Melo; Maria Luisa Paco-Larson; Gonçalo Guimarães Pereira; Neusa Pereira da Silva; Joao Bosco Pesquero; Juliana Gilbert Pessoa; Paula Rahal; Claudia Aparecida Rainho; Vanderlei Rodrigues; Silvia Regina Rogatto; Camila Malta Romano; Janaina Gusmao Romeiro; Benedito Mauro Rossi; Monica Rusticci; Renata Guerra de Sá; Simone Cristina Sant' Anna; Miriam L Sarmazo; Teresa Cristina de Lima E Silva; Fernando Augusto Soares; Maria de Fátima Sonati; Josane de Freitas Sousa; Diana Queiroz; Valéria Valente; André Luiz Vettore; Fabiola Elizabeth Villanova; Marco Antonio Zago; Heloisa Zalcberg
Journal:  Proc Natl Acad Sci U S A       Date:  2003-10-30       Impact factor: 11.205

8.  A novel human heparanase splice variant, T5, endowed with protumorigenic characteristics.

Authors:  Uri Barash; Victoria Cohen-Kaplan; Gil Arvatz; Svetlana Gingis-Velitski; Flonia Levy-Adam; Ofer Nativ; Ronen Shemesh; Michal Ayalon-Sofer; Neta Ilan; Israel Vlodavsky
Journal:  FASEB J       Date:  2009-12-09       Impact factor: 5.191

9.  A novel algorithm for computational identification of contaminated EST libraries.

Authors:  Rotem Sorek; Hershel M Safer
Journal:  Nucleic Acids Res       Date:  2003-02-01       Impact factor: 16.971

10.  Differential expression of novel adiponectin receptor-1 transcripts in skeletal muscle of subjects with normal glucose tolerance and type 2 diabetes.

Authors:  Reut Ashwal; Rina Hemi; Amir Tirosh; Reut Gordin; Eleanor Yissachar; Anat Cohen-Dayag; Avi Rosenberg; Avraham Karasik; Matthias Blüher; Hannah Kanety
Journal:  Diabetes       Date:  2011-02-02       Impact factor: 9.461
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