Coexpression cluster:C1921

Full id: C1921_small_Renal_Ciliary_Astrocyte_Lens_Meningeal_maxillary

Phase1 CAGE Peaks

Hg19::chr3:139258363..139258374,-	p4@RBP1
Hg19::chr3:139258382..139258393,-	p5@RBP1
Hg19::chr3:139258420..139258434,-	p3@RBP1
Hg19::chr3:139258443..139258485,-	p1@RBP1
Hg19::chr3:139258521..139258589,-	p2@RBP1

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
embryonic cell	1.47e-13	248
epithelial cell of nephron	1.47e-07	16
electrically responsive cell	2.19e-07	60
electrically active cell	2.19e-07	60
contractile cell	2.78e-07	59
ectodermal cell	9.75e-07	71

Uber Anatomy

Ontology term	p-value	n
cell layer	3.24e-31	312
multi-tissue structure	2.37e-30	347
epithelium	4.19e-30	309
organism subdivision	4.24e-26	365
anatomical conduit	1.15e-25	241
anatomical cluster	3.02e-24	286
ectoderm	5.01e-22	173
presumptive ectoderm	5.01e-22	173
ectoderm-derived structure	1.27e-21	169
multi-cellular organism	1.45e-21	659
tube	1.55e-21	194
embryo	2.62e-21	612
head	7.11e-21	123
neurectoderm	9.16e-20	90
anterior region of body	9.42e-20	129
craniocervical region	9.42e-20	129
neural plate	1.55e-19	86
presumptive neural plate	1.55e-19	86
regional part of nervous system	1.69e-19	94
nervous system	1.69e-19	94
embryonic structure	9.31e-19	605
developing anatomical structure	9.31e-19	605
central nervous system	1.36e-18	82
germ layer	2.51e-18	604
embryonic tissue	2.51e-18	604
presumptive structure	2.51e-18	604
epiblast (generic)	2.51e-18	604
anatomical system	5.89e-18	625
anatomical group	1.19e-17	626
brain	1.00e-14	69
future brain	1.00e-14	69
organ part	3.70e-14	219
trunk mesenchyme	1.03e-13	143
regional part of brain	1.31e-13	59
pre-chordal neural plate	1.50e-13	61
organ	1.94e-13	511
immaterial anatomical entity	7.30e-13	126
neural tube	1.45e-12	57
neural rod	1.45e-12	57
future spinal cord	1.45e-12	57
neural keel	1.45e-12	57
primordium	3.16e-11	168
epithelial tube	2.44e-10	118
mesenchyme	3.88e-10	238
entire embryonic mesenchyme	3.88e-10	238
trunk	4.38e-10	216
anatomical space	7.49e-10	104
adult organism	9.56e-10	115
compound organ	2.12e-09	69
trunk region element	2.21e-09	107
anatomical cavity	2.60e-09	70
body cavity precursor	4.83e-09	63
sensory system	6.85e-09	24
entire sense organ system	6.85e-09	24
sense organ	1.87e-08	23
intermediate mesoderm	2.22e-08	37
visual system	3.73e-08	21
regional part of forebrain	4.32e-08	41
forebrain	4.32e-08	41
future forebrain	4.32e-08	41
anterior neural tube	5.89e-08	42
excretory tube	6.88e-08	17
mesonephric epithelium	6.88e-08	17
mesonephric tubule	6.88e-08	17
nephric duct	6.88e-08	17
kidney epithelium	6.88e-08	17
renal duct	6.88e-08	17
mesonephric duct	6.88e-08	17
pronephric duct	6.88e-08	17
mesonephros	7.09e-08	18
pronephros	7.09e-08	18
nephrogenic cord	7.09e-08	18
pronephric mesoderm	7.09e-08	18
rostral part of nephrogenic cord	7.09e-08	18
presumptive pronephric mesoderm	7.09e-08	18
eye	1.02e-07	20
nephron epithelium	1.47e-07	16
nephron	1.47e-07	16
uriniferous tubule	1.47e-07	16
metanephric mesenchyme	1.47e-07	16
nephrogenic mesenchyme	1.47e-07	16
intraembryonic coelom	2.45e-07	21
camera-type eye	3.03e-07	19
simple eye	3.03e-07	19
ocular region	3.03e-07	19
optic cup	3.03e-07	19
eye primordium	3.03e-07	19
optic vesicle	3.03e-07	19
face	5.10e-07	21
abdomen element	5.55e-07	55
abdominal segment element	5.55e-07	55
unilaminar epithelium	7.74e-07	138

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	5	4.90738921487932	0.000351281809925646	0.0035337623720694
EBF1#1879	3	5.3438801079414	0.0118761556386811	0.0432443281064159
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135498531121203
TBP#6908	5	3.70677068709639	0.00142875510672112	0.00919848074163773
YY1#7528	5	4.91117074985386	0.0003499314082136	0.00352969734811861

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.