FANTOM5 summary Super-track Settings
 
FANTOM5 summary Tracks

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Enhancers  Enhancers (hg19)  Data version: FANTOM5 phase2.5
FANTOM-NET_Enhancers  FANTOM-NET Enhancers (hg19)  Data version: FANTOM5 NET
EnhProm_CellType  enhancer_promoter_correlations_distances_cell_type  Data version: FANTOM5 phase2.5
EnhProm_Organ  enhancer - promoter correlations distances organ  Data version: FANTOM5 phase2.5
TSS peaks  FANTOM5 DPI peak, robust set  Data version: FANTOM5 phase2.5
Total counts  Total counts of CAGE reads  Data version: FANTOM5 phase2.5
Max counts  Max counts of CAGE reads  Data version: FANTOM5 phase2.5
Data version: FANTOM5 phase2.5

Description - FANTOM5

Regulated transcription controls the diversity, developmental pathways, and spatial organization of the hundreds of cell types that make up a mammal. In FANTOM5 ( http://fantom.gsc.riken.jp/5/ ), we mapped transcription start sites (TSS) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of gene expression across the human body by using single molecule sequencing. This datahub is set up to provide the TSS activities in individual biological states and the identified regions. Please visit the web site for further data exploration and with details.

Methods

Protocol

Individual biological states are profiled by HeliScopeCAGE, which is a variation of CAGE (Cap Analysis Gene Expression) protocol based on a single molecule sequencer. The standard protocol requiring 5 µg of total RNA as a starting material is referred as hCAGE, and an optimized version for lower quantity (~ 100 ng) is referred as LQhCAGE (Kanamori-Katyama et al. 2011).

  • hCAGE
  • LQhCAGE

Samples

We mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. 5′-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. Individual samples shown in "TSS activity" tracks are grouped as below.

  • Primary cell
  • Tissue
  • Cell Line
  • Time course
  • Fractionation

TSS peaks and enhancers

TSS (CAGE) peaks across the panel of the biological states (samples) are identified by DPI (decomposition based peak identification, Forrest et al 2014), where each of the peaks consists of neighboring and related TSSs. The peaks are used as anchor to define promoters and as unit of promoter-level expression analysis. Two subsets of the peaks are defined based on evidence of read counts, depending on scopes of subsequent analyses, and the first subset (referred as robust set of the peaks, thresholded for expression analysis is shown as TSS peaks. They are named as "p#@GENE_SYMBOL" if associated with 5'-end of known genes, or "p@CHROM:START..END,STRAND" otherwise. The CAGE data is also used to produce an atlas of active, in vivo-transcribed enhancers (Andersson et al. 2014). The summary tracks consist of the TSS (CAGE) peaks, the enhancers, and summary profiles of TSS activities (total and maximum values). The summary track consists of the following tracks.

  • TSS (CAGE) peaks
    • the robust peaks
  • Enhancers
  • TSS summary profiles
    • Total counts and TPM (tags per million) in all the samples
    • Maximum counts and TPM among the samples

FANTOM-NET enhancers

A set of enhancers consist of the ones identified by Andersson et al. and the ones by Hirabayashi et al.

Credits

Please send us any questions regarding to this trackHub and underlying data.

References

  • The FANTOM5 project
  • Transcribed Enhancer Atlas
  • The FANTOM5 reprocessed data
  • Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, et al. Science. 2015 Feb 27;347(6225): 1010-4. doi: 10.1126/science.1259418. Epub 2015 [PMID: 25678556]
  • Gateways to the FANTOM5 promoter level mammalian expression atlas. Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S, et al. Genome Biol. 2015 Jan 5;16:22. doi: 10.1186/s13059-014-0560-6. [PMID: 25723102]
  • Unamplified cap analysis of gene expression on a single-molecule sequencer. Kanamori-Katayama M1, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO, Carninci P, Forrest AR, Hayashizaki Y.Genome Res. 2011 Jul;21(7):1150-9. [PMID: 21596820]
  • A promoter-level mammalian expression atlas. Forrest ARR, Kawaji H, Rehli M, Baillie JK, de Hoon MJL, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M et al. Nature. 2014 Mar 27;507(7493):462-70. [PMID: 24670764]
  • An atlas of active enhancers across human cell types and tissues. Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, et al. Nature. 2014 Mar 27;507(7493):455-61. [PMID: 24670763]
  • NET-CAGE Characterizes the Dynamics and Topology of Human Transcribed Cis-regulatory Elements. Hirabayashi S, Bhagat S, Matsuki Y, et al. in press.