Coexpression cluster:C3459

Full id: C3459_lung_pituitary_trachea_testis_medulla_caudate_glassy

Phase1 CAGE Peaks

Hg19::chr14:77843721..77843762,+	p1@SAMD15
Hg19::chr15:55790515..55790605,-	p3@CCPG1 p3@DYX1C1-CCPG1 p3@DYX1C1
Hg19::chr3:197676750..197676802,-	p1@IQCG

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><br>uberon_data<br>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	1.56e-21	94
nervous system	1.56e-21	94
central nervous system	3.16e-20	82
neural tube	1.28e-18	57
neural rod	1.28e-18	57
future spinal cord	1.28e-18	57
neural keel	1.28e-18	57
neurectoderm	1.10e-17	90
brain	2.52e-17	69
future brain	2.52e-17	69
regional part of forebrain	2.97e-17	41
forebrain	2.97e-17	41
future forebrain	2.97e-17	41
ectoderm	4.07e-17	173
presumptive ectoderm	4.07e-17	173
anterior neural tube	7.00e-17	42
neural plate	8.94e-17	86
presumptive neural plate	8.94e-17	86
regional part of brain	1.68e-16	59
ectoderm-derived structure	3.05e-16	169
organism subdivision	2.85e-15	365
head	2.98e-15	123
anterior region of body	2.10e-14	129
craniocervical region	2.10e-14	129
pre-chordal neural plate	2.36e-14	61
gray matter	6.17e-14	34
brain grey matter	6.17e-14	34
cerebral hemisphere	9.86e-14	32
telencephalon	9.96e-14	34
regional part of telencephalon	2.52e-13	33
cerebral cortex	1.32e-10	25
pallium	1.32e-10	25
multi-tissue structure	3.10e-10	347
regional part of cerebral cortex	6.27e-10	22
multi-cellular organism	6.99e-10	659
cell layer	4.75e-09	312
epithelium	7.38e-09	309
neocortex	8.14e-09	20
organ	1.62e-08	511
anatomical cluster	1.76e-08	286
anatomical system	6.49e-08	625
anatomical group	8.78e-08	626
anatomical conduit	3.71e-07	241
adult organism	5.15e-07	115
embryo	9.90e-07	612

Disease

Ontology term	p-value	n
cell type cancer	3.79e-17	143
carcinoma	4.80e-15	106
disease of cellular proliferation	1.10e-10	239
cancer	5.16e-10	235

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
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324420606755391
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.046112801176392
ELK4#2005	2	10.823787772312	0.0109128471951648	0.0401864126164738
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0153834759347707
GTF2B#2959	2	21.2958866228828	0.00287818058991141	0.015577255668226
MAX#4149	3	6.45255550900712	0.00372191383426551	0.01861652102188
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00719205963089263
POLR3A#11128	1	113.044036697248	0.0088200988100312	0.0334968108953036
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00483876385938894
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275977949240771
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328630541783693

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.