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Coexpression cluster:C2458

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Full id: C2458_Small_Keratinocyte_CD14_Urothelial_nasal_Mammary_Mallassezderived



Phase1 CAGE Peaks

Hg19::chr18:33058315..33058319,-p@chr18:33058315..33058319
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Hg19::chr18:33058490..33058501,-p@chr18:33058490..33058501
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Hg19::chr18:33058506..33058536,-p@chr18:33058506..33058536
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Hg19::chr18:33058547..33058592,-p@chr18:33058547..33058592
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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
mesoderm1.23e-08448
mesoderm-derived structure1.23e-08448
presumptive mesoderm1.23e-08448
embryonic structure1.82e-08605
developing anatomical structure1.82e-08605
germ layer1.90e-08604
embryonic tissue1.90e-08604
presumptive structure1.90e-08604
epiblast (generic)1.90e-08604
anatomical system2.30e-08625
bone marrow2.70e-0880
anatomical group3.53e-08626
skeletal element8.12e-08101
skeletal system8.12e-08101
embryo2.25e-07612
bone element8.35e-0786


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
CEBPB#105147.971147625824820.0002476385788090830.00268039439654283
EBF1#187948.9064668465690.00015887907472010.00199605096652142
EP300#203346.77394172622320.0004748459821442640.00434221517635626
FOS#235348.99795530889440.0001525147711168630.00194820085380064
FOSL2#2355416.93020060456171.2165416097647e-050.000303667278160171
FOXA1#3169411.08141974938556.62943068949433e-050.00107062179028931
HEY1#2346244.040111043105710.00375304636917980.018602079149104
HNF4A#3172317.34921777221530.0003125641557482750.00321519628308816
HNF4G#3174321.56506689483510.0001638032421292610.0020363583864704
JUN#3725412.51282919233634.07770316866756e-050.000742971460628875
JUNB#3726430.61063265982111.13787152942193e-064.65849332266944e-05
JUND#372746.994663941871030.000417684217818580.00391584578319162
NR3C1#2908414.9730233311731.98868032687801e-050.000443037083316579
RAD21#5885410.35503389545638.6948481184721e-050.00129356302371098
SMC3#9126415.04493284493281.95092670935632e-050.000437895625614581
SP1#666745.69838137814090.0009482606065333980.00684087790880303
SREBF1#6720447.00584944048832.04523668136926e-071.10161152019352e-05
SREBF2#67214436.9432624113482.70480926640298e-113.17045538691202e-09
STAT3#6774410.51946499715428.16377768286615e-050.00123121556306261
TAF1#687243.343046285745290.008005664898701650.0322160689074674
TBP#690843.706770687096390.005296377814784350.0244161731449244
TCF7L2#6934410.77017656313737.42969445082454e-050.00115451548690621



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.