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Coexpression cluster:C4731

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Full id: C4731_granulocyte_acute_osteosarcoma_thymus_smallcell_hippocampus_serous



Phase1 CAGE Peaks

Hg19::chr8:144450985..144451002,+p3@RHPN1
Hg19::chr8:144451007..144451031,+p2@RHPN1
Hg19::chr8:144451039..144451054,+p1@RHPN1


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>disease_data<br>


Cell Type
Ontology termp-valuen
epithelial cell6.30e-10254
Uber Anatomy
Ontology termp-valuen
neural tube4.18e-2057
neural rod4.18e-2057
future spinal cord4.18e-2057
neural keel4.18e-2057
adult organism6.77e-18115
central nervous system1.74e-1782
anterior neural tube3.74e-1742
regional part of forebrain4.36e-1741
forebrain4.36e-1741
future forebrain4.36e-1741
regional part of nervous system3.68e-1694
nervous system3.68e-1694
neurectoderm1.29e-1590
brain3.12e-1569
future brain3.12e-1569
regional part of brain9.10e-1559
neural plate1.04e-1486
presumptive neural plate1.04e-1486
gray matter2.67e-1434
brain grey matter2.67e-1434
telencephalon2.87e-1434
regional part of telencephalon7.88e-1433
cerebral hemisphere3.28e-1332
pre-chordal neural plate1.42e-1261
cerebral cortex9.44e-1025
pallium9.44e-1025
regional part of cerebral cortex9.75e-1022
neocortex1.04e-0820
anterior region of body4.82e-07129
craniocervical region4.82e-07129
trunk region element6.79e-07107
Disease
Ontology termp-valuen
carcinoma2.24e-18106
cell type cancer1.18e-15143
cancer1.53e-11235
disease of cellular proliferation1.32e-10239
adenocarcinoma5.19e-0925


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
CCNT2#90536.336201576962630.003930750035764890.0191234733770554
CEBPB#105137.971147625824820.001974187055288560.0115832652734428
CHD2#1106310.34402283411690.0009033701102746880.00663015256127745
E2F1#186934.907389214879320.008460985347239390.0327863182205526
E2F6#187635.017155731697390.00791769806886330.0324459102493139
EGR1#195834.988179094810140.008056488137383440.0322602394210639
ELF1#199734.258097958807540.01295179875054610.0465107763885529
ETS1#211339.728760922202340.001085840092584840.00765571143113939
FOS#235338.99795530889440.001372499272417130.0090220576228583
GABPB1#255337.067683836182170.002832212825417420.015485758613359
HMGN3#932438.178547723350590.001827766942164210.0109267402216765
IRF1#365937.63716375356390.002244692747297240.0128760073507429
IRF3#3661346.98195221148969.63568551583244e-060.000254255017581613
MXI1#460139.96157162875930.001011470541259020.00723640031912255
MYC#460935.22228187160940.007020843755740150.0296178818518296
NFKB1#479035.488063424193840.006049381815655430.0270910933255537
NFYA#4800318.42558069983050.0001598135507814160.0020027318730574
NFYB#4801316.75979325353650.0002123649923296180.00246764435179272
NRF1#4899312.21027944771090.0005492172401020010.00473655651024054
PBX3#5090321.91451268674419.49854535978121e-050.00137398695128835
SIN3A#2594235.408884726815140.006318961977991520.0278376036621865
SP1#666735.69838137814090.005403962701712170.0247950294615639
SP2#6668326.15353049384465.58768218891694e-050.000942765654488361
SREBF1#6720347.00584944048839.62099323994382e-060.000255416093794228
STAT3#6774310.51946499715420.0008589184530415310.00645821341376562
THAP1#55145331.36914460285133.23800758564397e-050.000649336164049675
USF1#739136.361499277207960.00388404057290560.0191251915791461
ZBTB7A#5134137.35190930787590.002516255860282270.0140977010778402



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.