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Coexpression cluster:C4686

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Full id: C4686_Monocytederived_CD14_Macrophage_smallcell_squamous_Basophils_signet



Phase1 CAGE Peaks

Hg19::chr7:36320649..36320687,+p4@EEPD1
Hg19::chr7:36320699..36320726,+p2@EEPD1
Hg19::chr7:36320733..36320746,+p9@EEPD1


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>


Uber Anatomy
Ontology termp-valuen
bone marrow3.28e-1976
bone element5.34e-1882
skeletal element1.77e-1490
hematopoietic system4.47e-1498
blood island4.47e-1498
immune system6.10e-1393
skeletal system3.90e-12100
hemolymphoid system2.41e-11108
neural tube1.06e-0956
neural rod1.06e-0956
future spinal cord1.06e-0956
neural keel1.06e-0956
nervous system2.08e-0989
central nervous system2.16e-0981
brain4.83e-0968
future brain4.83e-0968
regional part of nervous system5.21e-0953
regional part of brain5.21e-0953
organ1.51e-08503
brain grey matter7.68e-0834
gray matter7.68e-0834
telencephalon7.78e-0834
regional part of forebrain1.09e-0741
forebrain1.09e-0741
anterior neural tube1.09e-0741
future forebrain1.09e-0741
neural plate2.24e-0782
presumptive neural plate2.24e-0782
pre-chordal neural plate4.81e-0761
regional part of telencephalon7.82e-0732
cerebral hemisphere9.17e-0732


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#1066435.360256373075030.0064925092527670.0281310642984456
E2F1#186934.907389214879320.008460985347239390.0327717270686966
EBF1#187938.9064668465690.00141523283560980.00919188446009032
FOS#235338.99795530889440.001372499272417130.00901978678026507
FOSL2#2355316.93020060456170.0002060162053171620.00244113075415465
JUND#372736.994663941871030.002921845042734990.0157678176209476
MXI1#460139.96157162875930.001011470541259020.00723441801524113
NR3C1#2908314.9730233311730.0002978331194675480.00310216347502456
RAD21#5885310.35503389545630.0009004912073565420.0066856046921952
SMARCB1#6598318.25271578115740.000164397760679890.00204083415281672
SMARCC1#6599343.66335931963151.20046018043203e-050.000302618539184506



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.