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Coexpression cluster:C1916

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Full id: C1916_Fibroblast_amniotic_Adipocyte_Smooth_immature_CD14_normal



Phase1 CAGE Peaks

Hg19::chr3:105085383..105085403,+p7@ALCAM
Hg19::chr3:105085428..105085442,+p6@ALCAM
Hg19::chr3:105085548..105085584,+p2@ALCAM
Hg19::chr3:105085587..105085610,+p3@ALCAM
Hg19::chr3:105085734..105085760,+p1@ALCAM


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell4.20e-11180
fibroblast6.78e-1175
Uber Anatomy
Ontology termp-valuen
multi-cellular organism6.72e-13659
head1.84e-11123
anatomical system3.98e-11625
anatomical group7.47e-11626
organ8.73e-11511
organism subdivision7.31e-10365
embryonic structure7.46e-10605
developing anatomical structure7.46e-10605
germ layer8.53e-10604
embryonic tissue8.53e-10604
presumptive structure8.53e-10604
epiblast (generic)8.53e-10604
anterior region of body8.55e-10129
craniocervical region8.55e-10129
regional part of brain1.06e-0959
neural tube2.52e-0957
neural rod2.52e-0957
future spinal cord2.52e-0957
neural keel2.52e-0957
embryo5.42e-09612
neural plate1.12e-0886
presumptive neural plate1.12e-0886
brain2.51e-0869
future brain2.51e-0869
ectoderm-derived structure2.76e-08169
anatomical cluster3.50e-08286
neurectoderm5.62e-0890
ectoderm7.51e-08173
presumptive ectoderm7.51e-08173
pre-chordal neural plate9.61e-0861
regional part of forebrain1.28e-0741
forebrain1.28e-0741
future forebrain1.28e-0741
anterior neural tube1.31e-0742
gray matter2.50e-0734
brain grey matter2.50e-0734
telencephalon4.84e-0734
regional part of nervous system4.85e-0794
nervous system4.85e-0794
musculoskeletal system5.23e-07167
regional part of telencephalon6.45e-0733


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCF#1066455.360256373075030.0002259278299937090.00250060159354736
E2F1#186954.907389214879320.0003512818099256460.00353308175527971
E2F4#1874512.66806031528443.06319883889696e-060.00010356666349484
E2F6#187655.017155731697390.0003144978599297790.00323095042231027
ELF1#199754.258097958807540.0007142416939776840.00573584684946831
FOS#235358.99795530889441.69470025615156e-050.000389594541167098
GATA2#2624512.7449317335542.9719152914525e-060.000101234136048274
JUND#372745.595731153496820.001849593301755460.0109376408381201
MAX#414956.452555509007128.93743970843928e-050.00130749021671059
MYC#460955.22228187160940.0002573944848850610.00276706357250755
NFKB1#479055.488063424193840.0002008162847462320.00239254528434995
NR3C1#2908411.97841866493849.4122920812787e-050.00136643087667037
PAX5#507945.335652424942260.002223389586187790.0127811858758183
RAD21#5885510.35503389545638.39503550283973e-060.000229701103715242
SMC3#9126515.04493284493281.29633924985553e-065.16355358183302e-05
SP1#666755.69838137814090.000166391843712550.00204444679594059
TAF1#687253.343046285745290.002394600090870310.0135483850095024
TCF12#693836.380678941311850.007185168653258840.0298350758976503
USF1#739156.361499277207969.59569864925045e-050.00137020121852484
YY1#752854.911170749853860.00034993140821360.00352901567617035
ZNF143#7702410.80070124178230.0001415223430863190.00184455909017747



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.