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Coexpression cluster:C4267

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Full id: C4267_splenic_plasma_Burkitt_diffuse_xeroderma_b_migratory



Phase1 CAGE Peaks

Hg19::chr3:111852046..111852053,-p4@GCET2
Hg19::chr3:111852061..111852127,-p1@GCET2
Hg19::chr3:111852128..111852139,-p2@GCET2


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
lymphocyte2.25e-5153
common lymphoid progenitor2.25e-5153
lymphoid lineage restricted progenitor cell4.58e-5052
nucleate cell7.33e-4955
lymphocyte of B lineage1.35e-3224
pro-B cell1.35e-3224
leukocyte3.71e-32136
hematopoietic cell1.65e-29177
hematopoietic stem cell3.22e-29168
angioblastic mesenchymal cell3.22e-29168
nongranular leukocyte7.62e-27115
hematopoietic lineage restricted progenitor cell1.01e-25120
hematopoietic oligopotent progenitor cell5.11e-24161
hematopoietic multipotent progenitor cell5.11e-24161
B cell2.63e-1914
mature alpha-beta T cell8.92e-1818
alpha-beta T cell8.92e-1818
immature T cell8.92e-1818
mature T cell8.92e-1818
immature alpha-beta T cell8.92e-1818
T cell8.99e-1725
pro-T cell8.99e-1725
CD8-positive, alpha-beta T cell6.55e-1511
circulating cell1.86e-076
dendritic cell3.15e-0710
Uber Anatomy
Ontology termp-valuen
blood2.13e-0715
haemolymphatic fluid2.13e-0715
organism substance2.13e-0715
hemopoietic organ2.20e-077
immune organ2.20e-077
Disease
Ontology termp-valuen
lymphoma1.90e-0910


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
BCL11A#53335328.36945510360714.37778126761649e-050.000778894544818736
BCL3#602334.54710280373832.42397750207122e-050.000527631901498158
BCLAF1#9774321.65264761012189.8473954032885e-050.00139413329066565
CHD2#1106310.34402283411690.0009033701102746880.00661852479459686
EBF1#187938.9064668465690.00141523283560980.00917419788456659
ELF1#199734.258097958807540.01295179875054610.0463688780237311
EP300#203336.77394172622320.003216880500103790.0167891550922163
IRF4#3662321.91451268674419.49854535978121e-050.00137057001772615
MEF2A#4205318.74323090964410.0001518243905622470.00195227622826034
NFKB1#479035.488063424193840.006049381815655430.0270250400994627
NRF1#4899312.21027944771090.0005492172401020010.00472329540011635
PAX5#507936.669565531177830.003370290999677260.0173334230420689
POU2F2#545239.106124057742520.001324165192682130.00883896769516355
RAD21#5885310.35503389545630.0009004912073565420.00666098174127841
RFX5#5993312.04791082719510.0005717246050312580.00485765912991047
SIN3A#2594235.408884726815140.006318961977991520.0277614870443991
SMC3#9126315.04493284493280.0002935825420371870.00309899606911479
SP1#666735.69838137814090.005403962701712170.0247200937586666
SPI1#668838.204323508522730.001810593189410520.0109253837594664
STAT3#6774310.51946499715420.0008589184530415310.00644105581368597
TCF12#6938310.63446490218640.0008313523990202070.00630496065654429
YY1#752834.911170749853860.008441455341808260.0330292654894018
ZEB1#6935316.88843201754390.0002075486917327580.00243279212299411



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.