SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays

被引：21

作者：

Anton, Miguel A. ^{[1
,2
]}

Gorostiaga, Dorleta ^{[1
,2
]}

Guruceaga, Elizabeth ^{[1
,2
]}

Segura, Victor ^{[1
,2
]}

Carmona-Saez, Pedro ^{[3
]}

Pascual-Montano, Alberto ^{[4
]}

Pio, Ruben ^{[5
,6
]}

Montuenga, Luis M. ^{[6
,7
]}

Rubio, Angel ^{[1
,2
]}

机构：

[1] Univ Navarra, CEIT, San Sebastian, Spain

[2] Univ Navarra, TECNUN, San Sebastian, Spain

[3] Integrom SL, Madrid, Spain

[4] Univ Complutense Madrid, Fac Ciencias Fis, Comp Architecture Dept, E-28040 Madrid, Spain

[5] Univ Navarra, Dept Biochem, E-31080 Pamplona, Spain

[6] Univ Navarra, Ctr Appl Med Res, E-31080 Pamplona, Spain

[7] Univ Navarra, Dept Histol & Pathol, E-31080 Pamplona, Spain

来源：

GENOME BIOLOGY | 2008年 / 9卷 / 02期

关键词：

D O I：

10.1186/gb-2008-9-2-r46

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Exon and exon+junction microarrays are promising tools to study alternative splicing (AS). Current analytical tools applied to these arrays lack two relevant features: ability to predict unknown spliced forms and quantify the concentration of known and unknown isoforms. SPACE is an algorithm developed to 1) estimate the number of different transcripts expressed in several conditions, 2) predict the pre-mRNA splicing structure and 3) quantify the transcript concentrations including unknown forms. Results show its robustness and accuracy for real and simulated data.

引用

页数：41

共 30 条

[1] Profiling human phosphodiesterase genes and splice isoforms [J].

Bingham, Jonathan ;

Sudarsanam, Sucha ;

Srinivasan, Subha .

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2006, 350 (01) :25-32

[2] AN ANALYSIS OF TRANSFORMATIONS [J].

BOX, GEP ;

COX, DR .

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 1964, 26 (02) :211-252

[3] Alternative splicing and genome complexity [J].

Brett, D ;

Pospisil, H ;

Valcárcel, J ;

Reich, J ;

Bork, P .

NATURE GENETICS, 2002, 30 (01) :29-30

[4] Metagenes and molecular pattern discovery using matrix factorization [J].

Brunet, JP ;

Tamayo, P ;

Golub, TR ;

Mesirov, JP .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (12) :4164-4169

[5] Alternative splicing:: multiple control mechanisms and involvement in human disease [J].

Cáceres, JF ;

Kornblihtt, AR .

TRENDS IN GENETICS, 2002, 18 (04) :186-193

[6] Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing [J].

Castle, J ;

Garrett-Engele, P ;

Armour, CD ;

Duenwald, SJ ;

Loerch, PM ;

Meyer, MR ;

Schadt, EE ;

Stoughton, R ;

Parrish, ML ;

Shoemaker, DD ;

Johnson, JM .

GENOME BIOLOGY, 2003, 4 (10)

[7]

Cichocki A, 2006, LECT NOTES COMPUT SC, V3889, P32

[8]

Cichocki A, 2006, LECT NOTES COMPUT SC, V4029, P548, DOI 10.1007/11785231_58

[9] Data analysis of alternative splicing microarrays [J].

Cuperlovic-Culf, Miroslava ;

Belacel, Nabil ;

Culf, Adrian S. ;

Ouellette, Rodney J. .

DRUG DISCOVERY TODAY, 2006, 11 (21-22) :983-990

[10] Pre-mRNA splicing and human disease [J].

Faustino, NA ;

Cooper, TA .

GENES & DEVELOPMENT, 2003, 17 (04) :419-437

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