Large-scale clustering of CAGE tag expression data

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Shimokawa, Kazuro ^a   Okamura Oho, Yuko ^a   Kurita, Takio ^b   Frith, Martin C ^a,c   Kawai, Jun ^a,d   Carninci, Piero ^a,d   Hayashizaki, Yoshihide ^a,d  

^a RIKEN YOKOHAMA INSTITUTE   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c UNIVERSITY OF QUEENSLAND   (Australia)

^d RIKEN   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL FEATURES; CALCULATION COST; EXPRESSION DATA; EXPRESSION PROFILE; HIERARCHICAL CLUSTERING ALGORITHMS; NON-CODING RNAS; TISSUE-SPECIFIC PATTERNS; TRANSCRIPTION START SITE;

CELL CULTURE; CLUSTERING ALGORITHMS; GENES; MAMMALS; RNA; TISSUE ENGINEERING; TRANSCRIPTION;

TREES (MATHEMATICS);

RNA; UNTRANSLATED RNA; TRANSCRIPTION FACTOR;

ARTICLE; CELL LINE; CLUSTER ANALYSIS; COMPUTER PROGRAM; DATA ANALYSIS; DNA MICROARRAY; GENE CLUSTER; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE LOCATION; GENE MAPPING; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; NONHUMAN; SERIAL ANALYSIS OF GENE EXPRESSION; TISSUE SPECIFICITY; TISSUE TYPES; TRANSCRIPTION INITIATION; ALGORITHM; ANIMAL; CHROMOSOME MAP; DNA SEQUENCE; EVALUATION; EXPRESSED SEQUENCE TAG; GENETICS; METHODOLOGY; MOUSE; MULTIGENE FAMILY;

ALGORITHMS; ANIMALS; CHROMOSOME MAPPING; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; MICE; MULTIGENE FAMILY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION FACTORS;

EID: 34250170418     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-161     Document Type: Article

References (34)

1. Lockhart DJ Dong H Byrne MC Follettie MT Gallo MV Chee MS Mittmann M Wang C Kobayashi M Horton H Brown EL Expression monitoring by hybridization to high-density oligonucleotide arrays Nat Biotechnol 1996 13 1675-80 10.1038/nbt1296-1675
2. Schena M Shalon D Davis RW Brown PO Quantitative monitoring of gene expression patterns with a complementary DNA microarray Science 1995 270 5235 467-70 10.1126/science.270.5235.467 7569999
3. Velculescu VE Zhang L Vogelstein B Kinzler KW Serial analysis of gene expression Science 1995 270 5235 368-9 10.1126/science.270.5235.484 7569988
4. Saha S Sparks AB Rago C Akmaev V Wang CJ Vogelstein B Kinzler KW Velculescu VE Using the transcriptome to annotate the genome Nat Biotechnol 2002 20 5 508-12 10.1038/nbt0502-508 11981567
5. Kapranov P Cawley SE Drenkow J Bekiranov S Strausberg RL Fodor SP Gingeras TR Large-scale transcriptional activity in chromosomes 21 and 22 Science 2002 296 5569 916-9 10.1126/science.1068597 11988577
6. Eisen MB Spellman PT Brown PO Botstein D Cluster analysis and display of genome-wide expression patterns Proc Natl Acad Sci USA 1998 95 25 14863-8 24541 9843981 10.1073/pnas.95.25.14863
7. Miki R Kadota K Bono H Mizuno Y Tomaru Y Carninci P Itoh M Shibata K Kawai J Konno H Watanabe S Sato K Tokusumi Y Kikuchi N Ishii Y Hamaguchi Y Nishizuka I Goto H Nitanda H Satomi S Yoshiki A Kusakabe M DeRisi JL Eisen MB Iyer VR Brown PO Muramatsu M Shimada H Okazaki Y Hayashizaki Y Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays Proc Natl Acad Sci USA 2001 98 2199-204 30115 11226216 10.1073/ pnas.041605498
8. Shiraki T Kondo S Katayama S Waki K Kasukawa T Kawaji H Kodzius R Watahiki A Nakamura M Arakawa T Fukuda S Sasaki D Podhajska A Harbers M Kawai J Carninci P Hayashizaki Y Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage Proc Natl Acad Sci USA 2003 100 26 15776-81 307644 14663149 10.1073/pnas.2136655100
9. Carninci P Kasukawa T Katayama S Gough J Frith MC Maeda N Oyama R Ravasi T Lenhard B Wells C Kodzius R Shimokawa K Bajic VB Brenner SE Batalov S Forrest AR Zavolan M Davis MJ Wilming LG Aidinis V Allen JE Ambesi-Impiombato A Apweiler R Aturaliya RN Bailey TL Bansal M Baxter L Beisel KW Bersano T Bono H Chalk AM Chiu KP Choudhary V Christoffels A Clutterbuck DR Crowe ML Dalla E Dalrymple BP de Bono B Della Gatta G di Bernardo D Down T Engstrom P Fagiolini M Faulkner G Fletcher CF Fukushima T Furuno M Futaki S Gariboldi M Georgii-Hemming P Gingeras TR Gojobori T Green RE Gustincich S Harbers M Hayashi Y Hensch TK Hirokawa N Hill D Huminiecki L Iacono M Ikeo K Iwama A Ishikawa T Jakt M Kanapin A Katoh M Kawasawa Y Kelso J Kitamura H Kitano H Kollias G Krishnan SP Kruger A Kummerfeld SK Kurochkin IV Lareau LF Lazarevic D Lipovich L Liu J Liuni S McWilliam S Madan Babu M Madera M Marchionni L Matsuda H Matsuzawa S Miki H Mignone F Miyake S Morris K Mottagui-Tabar S Mulder N Nakano N Nakauchi H Ng P Nilsson R Nishiguchi S Nishikawa S Nori F Ohara O Okazaki Y Orlando V Pang KC Pavan WJ Pavesi G Pesole G Petrovsky N Piazza S Reed J Reid JF Ring BZ Ringwald M Rost B Ruan Y Salzberg SL Sandelin A Schneider C Schonbach C Sekiguchi K Semple CA Seno S Sessa L Sheng Y Shibata Y Shimada H Shimada K Silva D Sinclair B Sperling S Stupka E Sugiura K Sultana R Takenaka Y Taki K Tammoja K Tan SL Tang S Taylor MS Tegner J Teichmann SA Ueda HR van Nimwegen E Verardo R Wei CL Yagi K Yamanishi H Zabarovsky E Zhu S Zimmer A Hide W Bult C Grimmond SM Teasdale RD Liu ET Brusic V Quackenbush J Wahlestedt C Mattick JS Hume DA Kai C Sasaki D Tomaru Y Fukuda S Kanamori-Katayama M Suzuki M Aoki J Arakawa T Iida J Imamura K Itoh M Kato T Kawaji H Kawagashira N Kawashima T Kojima M Kondo S Konno H Nakano K Ninomiya N Nishio T Okada M Plessy C Shibata K Shiraki T Suzuki S Tagami M Waki K Watahiki A Okamura-Oho Y Suzuki H Kawai J Hayashizaki Y FANTOM Consortium; RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group) The transcriptional landscape of the mammalian genome Science 2005 309 5740 1559-63 10.1126/science.1112014 16141072
10. Zhang Y Xiong Y Yarbrough WG ARF promotes MDM2 degradation and stabilizes p53: ARF-INK4a locus deletion impairs both the Rb and p53 tumor suppression pathways Cell 1998 92 6 725-34 10.1016/ S0092-8674(00)81401-4 9529249
11. Stott FJ Bates S James MC McConnell BB Starborg M Brookes S Palmero I Ryan K Hara E Vousden KH Peters G The alternative product from the human CDKN2A locus, p14(ARF), participates in a regulatory feedback loop with p53 and MDM2 EMBO J 1998 17 17 5001-14 1170828 9724636 10.1093/emboj/ 17.17.5001
12. Kodzius R Matsumura Y Kasukawa T Shimokawa K Fukuda S Shiraki T Nakamura M Arakawa T Sasaki D Kawai J Harbers M Carninci P Hayashizaki Y Absolute expression values for mouse transcripts: Re-annotation of the READ expression database by the use of CAGE and EST sequence tags FEBS Lett 2004 559 1-3 22-6 10.1016/S0014-5793(04)00018-3 14960301
13. Okazaki Y Furuno M Kasukawa T Adachi J Bono H Kondo S Nikaido I Osato N Saito R Suzuki H Yamanaka I Kiyosawa H Yagi K Tomaru Y Hasegawa Y Nogami A Schonbach C Gojobori T Baldarelli R Hill DP Bult C Hume DA Quackenbush J Schriml LM Kanapin A Matsuda H Batalov S Beisel KW Blake JA Bradt D Brusic V Chothia C Corbani LE Cousins S Dalla E Dragani TA Fletcher CF Forrest A Frazer KS Gaasterland T Gariboldi M Gissi C Godzik A Gough J Grimmond S Gustincich S Hirokawa N Jackson IJ Jarvis ED Kanai A Kawaji H Kawasawa Y Kedzierski RM King BL Konagaya A Kurochkin IV Lee Y Lenhard B Lyons PA Maglott DR Maltais L Marchionni L McKenzie L Miki H Nagashima T Numata K Okido T Pavan WJ Pertea G Pesole G Petrovsky N Pillai R Pontius JU Qi D Ramachandran S Ravasi T Reed JC Reed DJ Reid J Ring BZ Ringwald M Sandelin A Schneider C Semple CA Setou M Shimada K Sultana R Takenaka Y Taylor MS Teasdale RD Tomita M Verardo R Wagner L Wahlestedt C Wang Y Watanabe Y Wells C Wilming LG Wynshaw-Boris A Yanagisawa M Yang I Yang L Yuan Z Zavolan M Zhu Y Zimmer A Carninci P Hayatsu N Hirozane-Kishikawa T Konno H Nakamura M Sakazume N Sato K Shiraki T Waki K Kawai J Aizawa K Arakawa T Fukuda S Hara A Hashizume W Imotani K Ishii Y Itoh M Kagawa I Miyazaki A Sakai K Sasaki D Shibata K Shinagawa A Yasunishi A Yoshino M Waterston R Lander ES Rogers J Birney E Hayashizaki Y FANTOM Consortium; RIKEN Genome Exploration Research Group Phase I & II Team Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs Nature 2002 420 563-73 10.1038/nature01266 12466851
14. Clare A King RD How well do we understand the clusters found in microarray data? In Silico Biol 2002 2 4 511-22 12611631
15. Tavazoie S Hughes JD Campbell MJ Cho RJ Church GM Systematic determination of genetic network architecture Nat Genet 1999 22 3 213-5 10.1038/10265 10391202
16. Cai L Huang H Blackshaw S Liu JS Cepko C Wong WH Clustering analysis of SAGE data using Poisson approach Genome Biol 2004 5 7 R51 463327 15239836 10.1186/gb-2004-5-7-r51
17. Anderberg MR Cluster Analysis for Applications New York: Academic Press 1973
18. Yeung KY Haynor DR Ruzzo WL Validating clustering for gene expression data Bioinformatics 2001 17 4 309-18 10.1093/bioinformatics/17.4.309 11301299
19. Kell DB King RD On the optimization of classes for the assignment of unidentified reading frames in functional genomics programmes: The need for machine learning Trends Biotechnol 2000 18 3 93-8 10.1016/ S0167-7799(99)01407-9 10675895
20. Akaike H A new look at the statistical model identification IEEE Trans Auto Control 1974 AC-19 6 716-23 10.1109/TAC.1974.1100705
21. Rissanen J A universal prior for integers and estimation by minimum description length Ann Stat 1983 11 2 416-31
22. Gene Ontology http://www.geneontology.org/
23. Berg JM Tymoczko JL Stryer L Clarke ND Biochemistry. "III. Synthesizing the Molecules of Life: 30.2. Each Organ Has a Unique Metabolic Profile" W.H. Freeman and Company 2001
24. Kurita T An efficient agglomerative clustering algorithm using a heap. Pattern Recognition 1991 24 3 205-209 10.1016/0031-3203(91)90062-A
25. Dash M Petrutiu S Scheuermann P Efficient Parallel Hierarchical Clustering International Europar Conference 2004 (EURO-PAR'04).
26. Tseng GC Wong WH Tight Clustering: A Resampling-based Approach for Identifying Stable and Tight Patterns in Data Biometrics 2005 61 10-16 10.1111/j.0006-341X.2005.031032.x 15737073
27. Carninci P Sandelin A Lenhard B Katayama S Shimokawa K Ponjavic J Semple CA Taylor MS Engstrom PG Frith MC Forrest AR Alkema WB Tan SL Plessy C Kodzius R Ravasi T Kasukawa T Fukuda S Kanamori-Katayama M Kitazume Y Kawaji H Kai C Nakamura M Konno H Nakano K Mottagui-Tabar S Arner P Chesi A Gustincich S Persichetti F Suzuki H Grimmond SM Wells CA Orlando V Wahlestedt C Liu ET Harbers M Kawai J Bajic VB Hume DA Hayashizaki Y Genome-wide analysis of mammalian promoter architecture and evolution Nat Genet 2006 38 6 626-35 10.1038/ng1789 16645617
28. FANTOM3 Basic Viewer http://gerg01.gsc.riken.jp/cage/mm5/ BrowseRnaLibrary.php
29. Kasukawa T Katayama S Kawaji H Suzuki H Hume DA Hayashizaki Y Construction of representative transcript and protein sets of human, mouse, and rat as a platform for their transcriptome and proteome analysis Genomics 2004 84 6 913-21 10.1016/j.ygeno.2004.08.011 15533708
30. R Statistics software http://www.r-project.org/
31. Supplementary web site http://gerg.gsc.riken.jp/2scluster/
32. Badger JH Olsen GJ CRITICA: Coding region identification tool invoking comparative analysis Mol Biol Evol 1999 16 4 512-24 10331277
33. Furuno M Kasukawa T Saito R Adachi J Suzuki H Baldarelli R Hayashizaki Y Okazaki Y CDS annotation in full-length cDNA sequence Genome Res 2003 13 6B 1478-87 403693 12819146 10.1101/gr.1060303
34. de Hoon MLJ Imoto S Nolan J Miyano S Open Source Clustering Software Bioinformatics 2004 20 9 1453-1454 10.1093/bioinformatics/bth078 14871861