Coexpression cluster:C3809

Full id: C3809_granulocyte_Astrocyte_Trabecular_acute_Meningeal_Renal_Myoblast

Phase1 CAGE Peaks

Hg19::chr19:4910094..4910138,+	p3@UHRF1
Hg19::chr19:4910143..4910175,+	p2@UHRF1
Hg19::chr19:4910177..4910205,+	p4@UHRF1

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
animal cell	1.29e-18	679
eukaryotic cell	1.29e-18	679
non-terminally differentiated cell	2.04e-18	180
native cell	4.78e-13	722
embryonic cell	1.79e-11	248
somatic cell	2.21e-10	591
fibroblast	7.38e-10	75
epithelial cell	6.17e-09	254
ectodermal cell	2.07e-08	71
neurectodermal cell	4.32e-08	59
migratory neural crest cell	1.11e-07	41
neural cell	3.39e-07	25
epithelial cell of nephron	5.74e-07	16

Uber Anatomy

Ontology term	p-value	n
anterior segment of eyeball	7.23e-08	14
camera-type eye	1.25e-07	19
simple eye	1.25e-07	19
ocular region	1.25e-07	19
optic cup	1.25e-07	19
eye primordium	1.25e-07	19
optic vesicle	1.25e-07	19
cell layer	1.35e-07	312
nephron epithelium	5.74e-07	16
nephron	5.74e-07	16
uriniferous tubule	5.74e-07	16
metanephric mesenchyme	5.74e-07	16
nephrogenic mesenchyme	5.74e-07	16
epithelium	6.83e-07	309
eye	7.49e-07	20
ectodermal placode	7.65e-07	29

Disease

Ontology term	p-value	n
cancer	3.68e-19	235
disease of cellular proliferation	8.47e-19	239
hematologic cancer	8.91e-18	51
immune system cancer	8.91e-18	51
leukemia	7.52e-17	39
myeloid leukemia	2.57e-14	31
organ system cancer	5.94e-11	137

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	3	6.33620157696263	0.00393075003576489	0.0190030830433389
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00660416288303081
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325376260652601
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00437206030771927
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.032061102140687
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00762277700003144
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00897460878487181
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154099231713347
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128070727033585
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00720284821072896
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.0019965032811077
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00245834487185912
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00471165593387653
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276741757881267
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246499152954279
SP2#6668	3	26.1535304938446	5.58768218891694e-05	0.000940183567147246
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.014018737106157

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.