Coexpression cluster:C969

Full id: C969_mature_insula_mesodermal_occipital_Preadipocyte_temporal_heart

Phase1 CAGE Peaks

Hg19::chr10:118502070..118502084,-	p1@HSPA12A
Hg19::chr15:62682733..62682759,+	p1@TLN2
Hg19::chr21:35014829..35014912,+	p1@ITSN1
Hg19::chr2:54683419..54683442,+	p2@SPTBN1
Hg19::chr2:54683448..54683470,+	p1@SPTBN1
Hg19::chr2:54684327..54684399,+	p4@SPTBN1
Hg19::chr9:131314859..131314877,+	p1@SPTAN1
Hg19::chr9:87285539..87285560,+	p21@NTRK2

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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p.value	FDR	nGenes	nPathway	Name
3.79490086907914e-05	0.0120108612506355	2	46	Interactions of the immunoglobulin superfamily (IgSF) member proteins (Reactome):REACT_23853
1.65551775624537e-06	0.00104794273970332	2	10	{SPTAN1,10} (Static Module):NA

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:0005200	structural constituent of cytoskeleton	4.99147211879799e-05
GO:0008091	spectrin	9.70308090475593e-05
GO:0030864	cortical actin cytoskeleton	0.000136243055220067
GO:0051693	actin filament capping	0.000136243055220067
GO:0051016	barbed-end actin filament capping	0.000136243055220067
GO:0030835	negative regulation of actin filament depolymerization	0.000136243055220067
GO:0030834	regulation of actin filament depolymerization	0.000136243055220067
GO:0030042	actin filament depolymerization	0.000136243055220067
GO:0030863	cortical cytoskeleton	0.000143580142384078
GO:0015629	actin cytoskeleton	0.000213216949059869
GO:0008064	regulation of actin polymerization and/or depolymerization	0.000290516615129923
GO:0044448	cell cortex part	0.000290516615129923
GO:0051261	protein depolymerization	0.000290516615129923
GO:0030832	regulation of actin filament length	0.000290516615129923
GO:0032535	regulation of cellular component size	0.000290516615129923
GO:0032956	regulation of actin cytoskeleton organization and biogenesis	0.000290516615129923
GO:0051129	negative regulation of cellular component organization and biogenesis	0.000335265835546014
GO:0051493	regulation of cytoskeleton organization and biogenesis	0.000343288446968344
GO:0033043	regulation of organelle organization and biogenesis	0.000343288446968344
GO:0003779	actin binding	0.000343288446968344
GO:0008154	actin polymerization and/or depolymerization	0.000374299671112961
GO:0005938	cell cortex	0.000393507614964763
GO:0008092	cytoskeletal protein binding	0.000771815799853878
GO:0051128	regulation of cellular component organization and biogenesis	0.000883182958994439
GO:0051248	negative regulation of protein metabolic process	0.000917108549270258
GO:0007010	cytoskeleton organization and biogenesis	0.00100030724883964
GO:0005516	calmodulin binding	0.00156030768475826
GO:0030036	actin cytoskeleton organization and biogenesis	0.00459280999558969
GO:0030029	actin filament-based process	0.00488493878915314
GO:0043121	neurotrophin binding	0.00488493878915314
GO:0048488	synaptic vesicle endocytosis	0.00567241467434988
GO:0016043	cellular component organization and biogenesis	0.00573061625175347
GO:0005856	cytoskeleton	0.00662604076192401
GO:0006996	organelle organization and biogenesis	0.00797412921710054
GO:0007016	cytoskeletal anchoring	0.0091139899944362
GO:0005886	plasma membrane	0.0091139899944362
GO:0051246	regulation of protein metabolic process	0.0100232053533945
GO:0030054	cell junction	0.0100807159878271
GO:0009892	negative regulation of metabolic process	0.0101401678185353
GO:0007043	intercellular junction assembly	0.0102515793004705
GO:0045216	intercellular junction assembly and maintenance	0.0125492597196398
GO:0048489	synaptic vesicle transport	0.0125492597196398
GO:0007028	cytoplasm organization and biogenesis	0.0163360075800794
GO:0044459	plasma membrane part	0.0196488111773652
GO:0005624	membrane fraction	0.0211664538902833
GO:0005925	focal adhesion	0.0215907385342878
GO:0005515	protein binding	0.0215907385342878
GO:0019717	synaptosome	0.0219321352358375
GO:0005924	cell-substrate adherens junction	0.0226747890717908
GO:0030055	cell-matrix junction	0.0233873930407654
GO:0001726	ruffle	0.0246430376281777
GO:0005912	adherens junction	0.0302912053126019
GO:0000267	cell fraction	0.0302912053126019
GO:0019538	protein metabolic process	0.0302912053126019
GO:0044430	cytoskeletal part	0.0302912053126019
GO:0043232	intracellular non-membrane-bound organelle	0.0302912053126019
GO:0043228	non-membrane-bound organelle	0.0302912053126019
GO:0065008	regulation of biological quality	0.0313083760599613
GO:0031252	leading edge	0.0355917882053961
GO:0016323	basolateral plasma membrane	0.0412782857834084
GO:0048523	negative regulation of cellular process	0.0417652213505117
GO:0019838	growth factor binding	0.0418142683574165
GO:0048519	negative regulation of biological process	0.0435488653287554
GO:0004714	transmembrane receptor protein tyrosine kinase activity	0.0495374653713563

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
fibroblast	3.84e-10	76
mesodermal cell	2.71e-07	121

Uber Anatomy

Ontology term	p-value	n
central nervous system	8.85e-30	81
anatomical cluster	1.68e-29	373
brain	1.09e-28	68
future brain	1.09e-28	68
adult organism	1.85e-28	114
neural tube	1.87e-28	56
neural rod	1.87e-28	56
future spinal cord	1.87e-28	56
neural keel	1.87e-28	56
nervous system	2.30e-28	89
structure with developmental contribution from neural crest	7.88e-28	132
regional part of nervous system	8.93e-27	53
regional part of brain	8.93e-27	53
tube	2.70e-25	192
anatomical conduit	9.35e-25	240
neural plate	2.38e-23	82
presumptive neural plate	2.38e-23	82
regional part of forebrain	2.38e-23	41
forebrain	2.38e-23	41
anterior neural tube	2.38e-23	41
future forebrain	2.38e-23	41
cell layer	5.03e-22	309
multi-tissue structure	9.41e-22	342
neurectoderm	1.51e-21	86
epithelium	1.93e-21	306
telencephalon	3.81e-20	34
brain grey matter	4.79e-20	34
gray matter	4.79e-20	34
cerebral hemisphere	3.48e-19	32
regional part of telencephalon	5.71e-19	32
ectoderm-derived structure	6.42e-19	171
ectoderm	6.42e-19	171
presumptive ectoderm	6.42e-19	171
multi-cellular organism	7.08e-17	656
pre-chordal neural plate	7.57e-17	61
ecto-epithelium	2.66e-16	104
organ system subdivision	2.87e-16	223
regional part of cerebral cortex	2.80e-15	22
cerebral cortex	5.90e-15	25
pallium	5.90e-15	25
anatomical system	9.89e-15	624
anatomical group	1.65e-14	625
neocortex	4.48e-14	20
organ part	5.27e-11	218
splanchnic layer of lateral plate mesoderm	8.27e-10	83
germ layer	3.38e-09	560
germ layer / neural crest	3.38e-09	560
embryonic tissue	3.38e-09	560
presumptive structure	3.38e-09	560
germ layer / neural crest derived structure	3.38e-09	560
epiblast (generic)	3.38e-09	560
developing anatomical structure	3.86e-09	581
embryonic structure	4.95e-09	564
embryo	6.05e-09	592
organ	7.42e-09	503
vasculature	1.93e-08	78
vascular system	1.93e-08	78
vessel	3.24e-07	68
epithelial tube open at both ends	3.71e-07	59
blood vessel	3.71e-07	59
blood vasculature	3.71e-07	59
vascular cord	3.71e-07	59
epithelial tube	4.31e-07	117
mesenchyme	5.58e-07	160
entire embryonic mesenchyme	5.58e-07	160
paraxial mesoderm	6.33e-07	72
presumptive paraxial mesoderm	6.33e-07	72
dense mesenchyme tissue	7.26e-07	73
primary circulatory organ	8.36e-07	27
basal ganglion	9.59e-07	9
nuclear complex of neuraxis	9.59e-07	9
aggregate regional part of brain	9.59e-07	9
collection of basal ganglia	9.59e-07	9
cerebral subcortex	9.59e-07	9

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	3.06711825929958	0.0112973236497416	0.0414473314594218
HEY1#23462	6	3.03008328232928	0.00400172346648327	0.0191889805838405
TAF1#6872	7	2.92516550002713	0.00126532535791574	0.0084934324220941
TAF7#6879	4	5.71653470246196	0.00306854155518016	0.0161774564099677
ZNF263#10127	5	5.13865102313167	0.00108253124903356	0.0076401190105295

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.