Coexpression cluster:C4085

Full id: C4085_chronic_acute_optic_medulloblastoma_Whole_mesothelioma_CD14CD16

Phase1 CAGE Peaks

Hg19::chr22:17082235..17082275,+	p@chr22:17082235..17082275 +
Hg19::chr22:17082352..17082382,+	p2@ENST00000558085
Hg19::chr22:17082732..17082775,+	p1@ENST00000558085

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><br>

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Cell Type

Ontology term	p-value	n
myeloid leukocyte	1.63e-19	76
myeloid lineage restricted progenitor cell	4.23e-18	70
granulocyte monocyte progenitor cell	4.48e-18	71
macrophage dendritic cell progenitor	5.21e-15	65
monopoietic cell	8.79e-15	63
monocyte	8.79e-15	63
monoblast	8.79e-15	63
promonocyte	8.79e-15	63
CD14-positive, CD16-negative classical monocyte	2.02e-14	42
myeloid cell	1.10e-13	112
common myeloid progenitor	1.10e-13	112
classical monocyte	5.63e-12	45

Uber Anatomy

Ontology term	p-value	n
adult organism	2.02e-25	115
hematopoietic system	1.65e-17	102
blood island	1.65e-17	102
bone marrow	1.95e-15	80
hemolymphoid system	6.11e-15	112
bone element	6.64e-13	86
lateral plate mesoderm	8.98e-12	216
skeletal element	4.52e-11	101
skeletal system	4.52e-11	101
musculoskeletal system	1.38e-08	167
neural plate	3.61e-08	86
presumptive neural plate	3.61e-08	86
neural tube	2.60e-07	57
neural rod	2.60e-07	57
future spinal cord	2.60e-07	57
neural keel	2.60e-07	57
neurectoderm	3.75e-07	90
immune system	4.42e-07	115

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
BCLAF1#9774	2	14.4350984067479	0.00620114743554613	0.027387898550387
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190356859401488
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322925945489129
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321210751891655
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463196558472857
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00763458014201345
FOSL1#8061	2	26.4757198109153	0.00186983370259098	0.0110261172189543
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00391860257194352
MAFK#7975	2	18.0671554252199	0.00398367474493681	0.0191138423616693
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.0072112070351936
REST#5978	3	9.65002871612802	0.00111263624711459	0.00768891795225307
SETDB1#9869	2	26.880017452007	0.00181446890796441	0.010894637132281
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277288264714057
SMC3#9126	2	10.0299552299552	0.012665637976747	0.0457616607158888
STAT1#6772	2	13.8043916647995	0.00677093170844408	0.0287552592996987
THAP1#55145	2	20.9127630685675	0.00298344741373694	0.0158706394561846
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329958888597295
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140487140913086

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.