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

Exon and exon+junction microarrays are promising tools for studying alternative splicing. Current analytical tools applied to these arrays lack two relevant features: the ability to predict unknown spliced forms and the ability to quantify the concentration of known and unknown isoforms. SPACE is an...

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Published inGenome biology Vol. 9; no. 2; pp. R46 - 1908
Main Authors Anton, Miguel A, Gorostiaga, Dorleta, Guruceaga, Elizabeth, Segura, Victor, Carmona-Saez, Pedro, Pascual-Montano, Alberto, Pio, Ruben, Montuenga, Luis M, Rubio, Angel
Format Journal Article
LanguageEnglish
Published London BioMed Central 29.02.2008
Subjects
Algorithms
Alternative Splicing
Animal Genetics and Genomics
Animals
Bioinformatics
Biomedical and Life Sciences
Computational Biology - methods
Computer Simulation
Evolutionary Biology
Exons
Human Genetics
Humans
Life Sciences
messenger RNA
Method
microarray technology
Microbial Genetics and Genomics
Oligonucleotide Array Sequence Analysis
Plant Genetics and Genomics
Protein Isoforms - genetics
RNA precursors
Transcription, Genetic
Additional Data File
Reverse Transcription Polymerase Chain Reaction
Exon Cassette
Multiplicative Noise
Probe Expression
Online AccessGet full text
ISSN1474-760X
1465-6906
1474-7596
1474-760X
1465-6914
DOI10.1186/gb-2008-9-2-r46

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Abstract Exon and exon+junction microarrays are promising tools for studying alternative splicing. Current analytical tools applied to these arrays lack two relevant features: the ability to predict unknown spliced forms and the ability to quantify the concentration of known and unknown isoforms. SPACE is an algorithm that has been developed to (1) estimate the number of different transcripts expressed under several conditions, (2) predict the precursor mRNA splicing structure and (3) quantify the transcript concentrations including unknown forms. The results presented here show its robustness and accuracy for real and simulated data.
AbstractList SPACE is an algorithm developed to predict and quantify the pre-mRNA splicing structure of transcripts using exon and ‘exon plus junction’ microarray data. Exon and exon+junction microarrays are promising tools for studying alternative splicing. Current analytical tools applied to these arrays lack two relevant features: the ability to predict unknown spliced forms and the ability to quantify the concentration of known and unknown isoforms. SPACE is an algorithm that has been developed to (1) estimate the number of different transcripts expressed under several conditions, (2) predict the precursor mRNA splicing structure and (3) quantify the transcript concentrations including unknown forms. The results presented here show its robustness and accuracy for real and simulated data.
Exon and exon+junction microarrays are promising tools for studying alternative splicing. Current analytical tools applied to these arrays lack two relevant features: the ability to predict unknown spliced forms and the ability to quantify the concentration of known and unknown isoforms. SPACE is an algorithm that has been developed to (1) estimate the number of different transcripts expressed under several conditions, (2) predict the precursor mRNA splicing structure and (3) quantify the transcript concentrations including unknown forms. The results presented here show its robustness and accuracy for real and simulated data.Exon and exon+junction microarrays are promising tools for studying alternative splicing. Current analytical tools applied to these arrays lack two relevant features: the ability to predict unknown spliced forms and the ability to quantify the concentration of known and unknown isoforms. SPACE is an algorithm that has been developed to (1) estimate the number of different transcripts expressed under several conditions, (2) predict the precursor mRNA splicing structure and (3) quantify the transcript concentrations including unknown forms. The results presented here show its robustness and accuracy for real and simulated data.
Exon and exon+junction microarrays are promising tools for studying alternative splicing. Current analytical tools applied to these arrays lack two relevant features: the ability to predict unknown spliced forms and the ability to quantify the concentration of known and unknown isoforms. SPACE is an algorithm that has been developed to (1) estimate the number of different transcripts expressed under several conditions, (2) predict the precursor mRNA splicing structure and (3) quantify the transcript concentrations including unknown forms. The results presented here show its robustness and accuracy for real and simulated data.
ArticleNumber R46
Author Guruceaga, Elizabeth
Pio, Ruben
Segura, Victor
Montuenga, Luis M
Pascual-Montano, Alberto
Anton, Miguel A
Rubio, Angel
Carmona-Saez, Pedro
Gorostiaga, Dorleta
AuthorAffiliation 1 CEIT and TECNUN, University of Navarra, San Sebastián, Spain
5 Department of Biochemistry, University of Navarra, Pamplona, Spain
4 Center for Applied Medical Research, University of Navarra, Pamplona, Spain
3 Computer Architecture Department, Facultad de Ciencias Físicas, Universidad Complutense de Madrid, Madrid 28040, Spain
2 Integromics SL, Madrid, Spain
6 Department of Histology and Pathology, University of Navarra, Pamplona, Spain
AuthorAffiliation_xml – name: 2 Integromics SL, Madrid, Spain
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Cites_doi 10.1038/44565
10.1101/gr.903503
10.1038/ng803
10.1038/418236a
10.1007/11785231_58
10.1093/bioinformatics/btl550
10.1016/j.dam.2005.09.021
10.1016/j.ymeth.2005.09.007
10.1016/j.drudis.2006.09.011
10.1073/pnas.0308531101
10.1038/35057062
10.1186/gb-2003-4-10-r66
10.1038/nbt964
10.1038/sj.onc.1207362
10.1186/1471-2105-7-366
10.1093/bioinformatics/btg1044
10.1016/j.csda.2005.09.010
10.1109/TPAMI.2006.60
10.1007/11679363_5
10.1016/S1470-2045(07)70104-3
10.1016/S0168-9525(01)02626-9
10.1126/science.1090100
10.1093/bioinformatics/btk028
10.1016/j.bbrc.2006.08.180
10.1111/j.2517-6161.1964.tb00553.x
10.1093/nar/gni047
10.1101/gad.1048803
10.1073/pnas.98.1.31
10.1093/nar/gnh173
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Keywords Additional Data File
Reverse Transcription Polymerase Chain Reaction
Exon Cassette
Multiplicative Noise
Probe Expression
Language English
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References PM Kim (1908_CR27) 2003; 13
J Castle (1908_CR11) 2003; 4
DD Lee (1908_CR19) 2001; 13
International Human Genome Sequencing Consortium (1908_CR2) 2001; 409
NA Faustino (1908_CR5) 2003; 17
P Fehlbaum (1908_CR14) 2005; 33
K Le (1908_CR15) 2004; 32
A Pascual-Montano (1908_CR22) 2006; 28
A Pascual-Montano (1908_CR26) 2006; 7
JF Caceres (1908_CR4) 2002; 18
MA Garcia-Blanco (1908_CR6) 2004; 22
T Maniatis (1908_CR1) 2002; 418
M Zhu (1908_CR28) 2006; 51
D Brett (1908_CR3) 2002; 30
A Cichocki (1908_CR21) 2006
H Wang (1908_CR10) 2003; 19
P Fogel (1908_CR29) 2007; 23
GW Klau (1908_CR20) 2006; 155
JP Brunet (1908_CR25) 2004; 101
M Cuperlovic-Culf (1908_CR17) 2006; 11
L Hui (1908_CR8) 2004; 23
JM Johnson (1908_CR9) 2003; 302
J Bingham (1908_CR16) 2006; 350
A Cichocki (1908_CR24) 2006
K Srinivasan (1908_CR13) 2005; 37
DD Lee (1908_CR18) 1999; 401
MJ Pajares (1908_CR7) 2007; 8
O Shai (1908_CR12) 2006; 22
C Li (1908_CR23) 2001; 98
GEP Box (1908_CR30) 1964; 26
15048092 - Oncogene. 2004 Apr 15;23(17):3013-23
16526426 - IEEE Trans Pattern Anal Mach Intell. 2006 Mar;28(3):403-15
15598820 - Nucleic Acids Res. 2004;32(22):e180
12600935 - Genes Dev. 2003 Feb 15;17(4):419-37
12840046 - Genome Res. 2003 Jul;13(7):1706-18
11932019 - Trends Genet. 2002 Apr;18(4):186-93
16403798 - Bioinformatics. 2006 Mar 1;22(5):606-13
16875499 - BMC Bioinformatics. 2006;7:366
16314264 - Methods. 2005 Dec;37(4):345-59
11134512 - Proc Natl Acad Sci U S A. 2001 Jan 2;98(1):31-6
11237011 - Nature. 2001 Feb 15;409(6822):860-921
17092989 - Bioinformatics. 2007 Jan 1;23(1):44-9
14519201 - Genome Biol. 2003;4(10):R66
11743582 - Nat Genet. 2002 Jan;30(1):29-30
10548103 - Nature. 1999 Oct 21;401(6755):788-91
15760843 - Nucleic Acids Res. 2005;33(5):e47
12110900 - Nature. 2002 Jul 11;418(6894):236-43
12855476 - Bioinformatics. 2003;19 Suppl 1:i315-22
14684825 - Science. 2003 Dec 19;302(5653):2141-4
16987497 - Biochem Biophys Res Commun. 2006 Nov 10;350(1):25-32
17395108 - Lancet Oncol. 2007 Apr;8(4):349-57
15122293 - Nat Biotechnol. 2004 May;22(5):535-46
15016911 - Proc Natl Acad Sci U S A. 2004 Mar 23;101(12):4164-9
17055407 - Drug Discov Today. 2006 Nov;11(21-22):983-90
References_xml – volume: 401
  start-page: 788
  year: 1999
  ident: 1908_CR18
  publication-title: Nature
  doi: 10.1038/44565
– volume: 13
  start-page: 1706
  year: 2003
  ident: 1908_CR27
  publication-title: Genome Res
  doi: 10.1101/gr.903503
– volume: 30
  start-page: 29
  year: 2002
  ident: 1908_CR3
  publication-title: Nat Genet
  doi: 10.1038/ng803
– volume: 418
  start-page: 236
  year: 2002
  ident: 1908_CR1
  publication-title: Nature
  doi: 10.1038/418236a
– start-page: 548
  volume-title: Proceedings of the Internationl Conference on Artificial Intelligence and Soft Computing (ICAISC 2006): 25-29 June 2006; Zakopane, Poland
  year: 2006
  ident: 1908_CR21
  doi: 10.1007/11785231_58
– volume: 23
  start-page: 44
  year: 2007
  ident: 1908_CR29
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btl550
– volume: 155
  start-page: 840
  year: 2006
  ident: 1908_CR20
  publication-title: Discrete Appl Math
  doi: 10.1016/j.dam.2005.09.021
– volume: 37
  start-page: 345
  year: 2005
  ident: 1908_CR13
  publication-title: Methods
  doi: 10.1016/j.ymeth.2005.09.007
– volume: 11
  start-page: 983
  year: 2006
  ident: 1908_CR17
  publication-title: Drug Discov Today
  doi: 10.1016/j.drudis.2006.09.011
– volume: 101
  start-page: 4164
  year: 2004
  ident: 1908_CR25
  publication-title: Proc Natl Acad Sci USA
  doi: 10.1073/pnas.0308531101
– volume: 409
  start-page: 860
  year: 2001
  ident: 1908_CR2
  publication-title: Nature
  doi: 10.1038/35057062
– volume: 4
  start-page: R66
  year: 2003
  ident: 1908_CR11
  publication-title: Genome Biol
  doi: 10.1186/gb-2003-4-10-r66
– volume: 22
  start-page: 535
  year: 2004
  ident: 1908_CR6
  publication-title: Nat Biotechnol
  doi: 10.1038/nbt964
– volume: 23
  start-page: 3013
  year: 2004
  ident: 1908_CR8
  publication-title: Oncogene
  doi: 10.1038/sj.onc.1207362
– volume: 7
  start-page: 366
  year: 2006
  ident: 1908_CR26
  publication-title: BMC Bioinformatics
  doi: 10.1186/1471-2105-7-366
– volume: 19
  start-page: i315
  issue: Suppl 1
  year: 2003
  ident: 1908_CR10
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btg1044
– volume: 51
  start-page: 918
  year: 2006
  ident: 1908_CR28
  publication-title: Comput Stat Data Anal
  doi: 10.1016/j.csda.2005.09.010
– volume: 28
  start-page: 403
  year: 2006
  ident: 1908_CR22
  publication-title: IEEE Trans Pattern Anal Mach Intell
  doi: 10.1109/TPAMI.2006.60
– start-page: 32
  volume-title: Proceedings of Independent Component Analysis and Blind Signal Separation (ICA 2006): 5-8 March 2006; Charleston, SC
  year: 2006
  ident: 1908_CR24
  doi: 10.1007/11679363_5
– volume: 8
  start-page: 349
  year: 2007
  ident: 1908_CR7
  publication-title: Lancet Oncol
  doi: 10.1016/S1470-2045(07)70104-3
– volume: 18
  start-page: 186
  year: 2002
  ident: 1908_CR4
  publication-title: Trends Genet
  doi: 10.1016/S0168-9525(01)02626-9
– volume: 302
  start-page: 2141
  year: 2003
  ident: 1908_CR9
  publication-title: Science
  doi: 10.1126/science.1090100
– volume: 22
  start-page: 606
  year: 2006
  ident: 1908_CR12
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btk028
– volume: 350
  start-page: 25
  year: 2006
  ident: 1908_CR16
  publication-title: Biochem Biophys Res Commun
  doi: 10.1016/j.bbrc.2006.08.180
– volume: 26
  start-page: 211
  year: 1964
  ident: 1908_CR30
  publication-title: J Roy Statist Soc B (Statist Meth)
  doi: 10.1111/j.2517-6161.1964.tb00553.x
– volume: 13
  start-page: 556
  year: 2001
  ident: 1908_CR19
  publication-title: Adv Neural Inf Process Syst
– volume: 33
  start-page: e47
  year: 2005
  ident: 1908_CR14
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gni047
– volume: 17
  start-page: 419
  year: 2003
  ident: 1908_CR5
  publication-title: Genes Dev
  doi: 10.1101/gad.1048803
– volume: 98
  start-page: 31
  year: 2001
  ident: 1908_CR23
  publication-title: Proc Natl Acad Sci USA
  doi: 10.1073/pnas.98.1.31
– volume: 32
  start-page: e180
  year: 2004
  ident: 1908_CR15
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gnh173
– reference: 15598820 - Nucleic Acids Res. 2004;32(22):e180
– reference: 16526426 - IEEE Trans Pattern Anal Mach Intell. 2006 Mar;28(3):403-15
– reference: 11743582 - Nat Genet. 2002 Jan;30(1):29-30
– reference: 15016911 - Proc Natl Acad Sci U S A. 2004 Mar 23;101(12):4164-9
– reference: 16987497 - Biochem Biophys Res Commun. 2006 Nov 10;350(1):25-32
– reference: 12855476 - Bioinformatics. 2003;19 Suppl 1:i315-22
– reference: 15122293 - Nat Biotechnol. 2004 May;22(5):535-46
– reference: 11237011 - Nature. 2001 Feb 15;409(6822):860-921
– reference: 16875499 - BMC Bioinformatics. 2006;7:366
– reference: 15048092 - Oncogene. 2004 Apr 15;23(17):3013-23
– reference: 17055407 - Drug Discov Today. 2006 Nov;11(21-22):983-90
– reference: 12600935 - Genes Dev. 2003 Feb 15;17(4):419-37
– reference: 17092989 - Bioinformatics. 2007 Jan 1;23(1):44-9
– reference: 12840046 - Genome Res. 2003 Jul;13(7):1706-18
– reference: 12110900 - Nature. 2002 Jul 11;418(6894):236-43
– reference: 14519201 - Genome Biol. 2003;4(10):R66
– reference: 11134512 - Proc Natl Acad Sci U S A. 2001 Jan 2;98(1):31-6
– reference: 10548103 - Nature. 1999 Oct 21;401(6755):788-91
– reference: 15760843 - Nucleic Acids Res. 2005;33(5):e47
– reference: 17395108 - Lancet Oncol. 2007 Apr;8(4):349-57
– reference: 11932019 - Trends Genet. 2002 Apr;18(4):186-93
– reference: 14684825 - Science. 2003 Dec 19;302(5653):2141-4
– reference: 16314264 - Methods. 2005 Dec;37(4):345-59
– reference: 16403798 - Bioinformatics. 2006 Mar 1;22(5):606-13
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Snippet Exon and exon+junction microarrays are promising tools for studying alternative splicing. Current analytical tools applied to these arrays lack two relevant...
SPACE is an algorithm developed to predict and quantify the pre-mRNA splicing structure of transcripts using exon and 'exon plus junction' microarray data....
SPACE is an algorithm developed to predict and quantify the pre-mRNA splicing structure of transcripts using exon and ‘exon plus junction’ microarray data....
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StartPage R46
SubjectTerms Algorithms
Alternative Splicing
Animal Genetics and Genomics
Animals
Bioinformatics
Biomedical and Life Sciences
Computational Biology - methods
Computer Simulation
Evolutionary Biology
Exons
Human Genetics
Humans
Life Sciences
messenger RNA
Method
microarray technology
Microbial Genetics and Genomics
Oligonucleotide Array Sequence Analysis
Plant Genetics and Genomics
Protein Isoforms - genetics
RNA precursors
Transcription, Genetic
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Title SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays
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