Coexpression cluster:C4267

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

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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

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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>

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Cell Type

Ontology term	p-value	n
hematopoietic stem cell	7.82e-37	172
angioblastic mesenchymal cell	7.82e-37	172
lymphocyte	2.76e-36	53
common lymphoid progenitor	2.76e-36	53
lymphoid lineage restricted progenitor cell	2.18e-35	52
hematopoietic cell	4.63e-35	182
leukocyte	2.70e-34	140
hematopoietic oligopotent progenitor cell	1.54e-32	165
hematopoietic multipotent progenitor cell	1.54e-32	165
hematopoietic lineage restricted progenitor cell	1.45e-28	124
nongranular leukocyte	1.18e-27	119
lymphocyte of B lineage	1.40e-21	24
pro-B cell	1.40e-21	24
T cell	2.09e-13	25
pro-T cell	2.09e-13	25
B cell	4.98e-13	14
mature alpha-beta T cell	6.41e-13	18
alpha-beta T cell	6.41e-13	18
immature T cell	6.41e-13	18
mature T cell	6.41e-13	18
immature alpha-beta T cell	6.41e-13	18
CD8-positive, alpha-beta T cell	6.17e-10	11
dendritic cell	4.04e-08	10
myeloid cell	4.21e-07	112
common myeloid progenitor	4.21e-07	112
conventional dendritic cell	5.13e-07	8

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	2.44e-11	102
blood island	2.44e-11	102
blood	3.22e-11	15
haemolymphatic fluid	3.22e-11	15
organism substance	3.22e-11	15
hemolymphoid system	5.00e-10	112
adult organism	3.45e-07	115

Disease

Ontology term	p-value	n
hematologic cancer	9.74e-08	51
immune system cancer	9.74e-08	51
lymphoma	4.89e-07	10

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

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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

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

TF	#promoters	Enrichment	p-value	q-value
BCL11A#53335	3	28.3694551036071	4.37778126761649e-05	0.000778894544818736
BCL3#602	3	34.5471028037383	2.42397750207122e-05	0.000527631901498158
BCLAF1#9774	3	21.6526476101218	9.8473954032885e-05	0.00139413329066565
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00661852479459686
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00917419788456659
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463688780237311
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167891550922163
IRF4#3662	3	21.9145126867441	9.49854535978121e-05	0.00137057001772615
MEF2A#4205	3	18.7432309096441	0.000151824390562247	0.00195227622826034
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270250400994627
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00472329540011635
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173334230420689
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00883896769516355
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00666098174127841
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00485765912991047
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277614870443991
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00309899606911479
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247200937586666
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109253837594664
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00644105581368597
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00630496065654429
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330292654894018
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00243279212299411

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

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This analysis result is provided for C0 - C305 clusters.