Coexpression cluster:C1299

Full id: C1299_chronic_acute_chorionic_leukemia_choriocarcinoma_pancreatic_placenta

Phase1 CAGE Peaks

Hg19::chr10:11936692..11936705,-	p1@ENST00000445498 p1@uc001iky.1
Hg19::chr11:64937702..64937707,+	p1@SPDYC
Hg19::chr2:12417696..12417715,-	p@chr2:12417696..12417715 -
Hg19::chr2:15696037..15696048,-	p@chr2:15696037..15696048 -
Hg19::chr8:129061640..129061667,+	p@chr8:129061640..129061667 +
Hg19::chr8:129061678..129061731,+	p@chr8:129061678..129061731 +

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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GO ID	GO name	FDR corrected p-value
GO:0019901	protein kinase binding	0.0189420699399505
GO:0019900	kinase binding	0.0189420699399505
GO:0019899	enzyme binding	0.0389045880921543

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
myeloid cell	7.27e-46	112
common myeloid progenitor	7.27e-46	112
hematopoietic stem cell	1.62e-36	172
angioblastic mesenchymal cell	1.62e-36	172
hematopoietic cell	3.95e-36	182
hematopoietic oligopotent progenitor cell	8.55e-36	165
hematopoietic multipotent progenitor cell	8.55e-36	165
myeloid leukocyte	7.95e-32	76
myeloid lineage restricted progenitor cell	1.62e-31	70
granulocyte monocyte progenitor cell	2.80e-30	71
macrophage dendritic cell progenitor	4.01e-27	65
CD14-positive, CD16-negative classical monocyte	9.68e-27	42
monopoietic cell	3.30e-26	63
monocyte	3.30e-26	63
monoblast	3.30e-26	63
promonocyte	3.30e-26	63
classical monocyte	1.17e-23	45
leukocyte	5.34e-23	140
hematopoietic lineage restricted progenitor cell	3.47e-22	124
nongranular leukocyte	5.88e-19	119
intermediate monocyte	9.81e-08	9
CD14-positive, CD16-positive monocyte	9.81e-08	9

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	6.23e-32	102
blood island	6.23e-32	102
hemolymphoid system	6.24e-27	112
bone marrow	7.16e-24	80
bone element	4.13e-21	86
immune system	7.35e-19	115
lateral plate mesoderm	6.25e-18	216
skeletal element	2.13e-14	101
skeletal system	2.13e-14	101
blood	2.73e-09	15
haemolymphatic fluid	2.73e-09	15
organism substance	2.73e-09	15

Disease

Ontology term	p-value	n
myeloid leukemia	1.79e-16	31
leukemia	2.67e-13	39
hematologic cancer	1.06e-09	51
immune system cancer	1.06e-09	51

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
CCNT2#905	5	5.28016798080219	0.000510094397483253	0.00446627672524761
FOS#2353	4	5.99863687259627	0.00189982371188635	0.0111814983739475
FOSL1#8061	3	19.8567898581865	0.000301402757252219	0.00310987972383565
GATA1#2623	3	6.78015407190022	0.00676576398334856	0.0287426628968817
GATA2#2624	3	6.372465866777	0.00805882130874255	0.0318808802524153
GTF2B#2959	2	10.6479433114414	0.0135134586576011	0.0477220568317173
JUN#3725	3	6.25641459616817	0.00848634685095487	0.0324036845118045
MAX#4149	4	4.30170367267141	0.00664492391067637	0.0282902942524613
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.037979435002417
REST#5978	4	6.43335247741868	0.00145495422303207	0.00932347307026914
STAT2#6773	3	32.6318855932203	6.94270331437341e-05	0.00110095504319746
TAF1#6872	5	2.78587190478774	0.0107863634029041	0.0397823571506832
TAL1#6886	3	14.9343083387201	0.000695218440592151	0.00559771171975974
TBP#6908	5	3.08897557258032	0.00664544827578693	0.0282775412514224
THAP1#55145	2	10.4563815342838	0.0139914785110365	0.0491145477350815

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.