title: Large-scale clustering of CAGE tag expression data.
abstract: BACKGROUND
  Recent analyses have suggested that many genes possess multiple transcription start sites (TSSs) that are differentially utilized in different tissues and cell lines. We have identified a huge number of TSSs mapped onto the mouse genome using the cap analysis of gene expression (CAGE) method. The standard hierarchical clustering algorithm, which gives us easily understandable graphical tree images, has difficulties in processing such huge amounts of TSS data and a better method to calculate and display the results is needed.
  
  
  RESULTS
  We use a combination of hierarchical and non-hierarchical clustering to cluster expression profiles of TSSs based on a large amount of CAGE data to profit from the best of both methods. We processed the genome-wide expression data, including 159,075 TSSs derived from 127 RNA samples of various organs of mouse, and succeeded in categorizing them into 70-100 clusters. The clusters exhibited intriguing biological features: a cluster supergroup with a ubiquitous expression profile, tissue-specific patterns, a distinct distribution of non-coding RNA and functional TSS groups.
  
  
  CONCLUSIONS
  Our approach succeeded in greatly reducing the calculation cost, and is an appropriate solution for analyzing large-scale TSS usage data.
authors.affiliation: Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan. kazsi@gsc.riken.jp
authors.forename: Kazuro
authors.initials: K
authors.lastname: Shimokawa
authors.forename: Yuko
authors.initials: Y
authors.lastname: Okamura-Oho
authors.forename: Takio
authors.initials: T
authors.lastname: Kurita
authors.forename: Martin C
authors.initials: MC
authors.lastname: Frith
authors.forename: Jun
authors.initials: J
authors.lastname: Kawai
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
mesh_terms: D000465:Algorithms; D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods*; D051379:Mice; D005810:Multigene Family / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D014157:Transcription Factors