Coexpression cluster:C879

Full id: C879_Osteoblast_Adipocyte_Olfactory_leiomyoma_Smooth_tenocyte_Fibroblast

Phase1 CAGE Peaks

Hg19::chr11:119289293..119289305,-	p12@THY1
Hg19::chr11:119289671..119289701,-	p10@THY1
Hg19::chr11:119289738..119289754,-	p9@THY1
Hg19::chr11:119290792..119290808,-	p4@BC009328
Hg19::chr11:119290830..119290845,-	p6@BC009328
Hg19::chr11:119290894..119290943,-	p1@BC009328
Hg19::chr11:119291028..119291044,-	p3@BC009328
Hg19::chr11:119291053..119291082,-	p2@BC009328
Hg19::chr11:119291603..119291653,-	p4@THY1

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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GO ID	GO name	FDR corrected p-value
GO:0051281	positive regulation of release of sequestered calcium ion into cytosol	0.00232123933996064
GO:0046549	retinal cone cell development	0.00232123933996064
GO:0042670	retinal cone cell differentiation	0.00232123933996064
GO:0060042	retina morphogenesis in camera-type eye	0.00232123933996064
GO:0050860	negative regulation of T cell receptor signaling pathway	0.00232123933996064
GO:0051279	regulation of release of sequestered calcium ion into cytosol	0.00232123933996064
GO:0050858	negative regulation of antigen receptor-mediated signaling pathway	0.00232123933996064
GO:0060041	retina development in camera-type eye	0.00254881182427051
GO:0042462	eye photoreceptor cell development	0.00254881182427051
GO:0043547	positive regulation of GTPase activity	0.00254881182427051
GO:0050771	negative regulation of axonogenesis	0.00254881182427051
GO:0050856	regulation of T cell receptor signaling pathway	0.00254881182427051
GO:0001754	eye photoreceptor cell differentiation	0.00254881182427051
GO:0051283	negative regulation of sequestering of calcium ion	0.00254881182427051
GO:0042461	photoreceptor cell development	0.00254881182427051
GO:0051282	regulation of sequestering of calcium ion	0.00254881182427051
GO:0051209	release of sequestered calcium ion into cytosol	0.00254881182427051
GO:0051208	sequestering of calcium ion	0.00270811256328741
GO:0046530	photoreceptor cell differentiation	0.00270811256328741
GO:0050854	regulation of antigen receptor-mediated signaling pathway	0.00270811256328741
GO:0050768	negative regulation of neurogenesis	0.00293378861022803
GO:0048593	camera-type eye morphogenesis	0.00293378861022803
GO:0048041	focal adhesion formation	0.00293378861022803
GO:0051238	sequestering of metal ion	0.00293378861022803
GO:0050852	T cell receptor signaling pathway	0.00367529562160434
GO:0030426	growth cone	0.00367529562160434
GO:0030336	negative regulation of cell migration	0.00367529562160434
GO:0030427	site of polarized growth	0.00367529562160434
GO:0051271	negative regulation of cell motility	0.00419320654960631
GO:0005100	Rho GTPase activator activity	0.00419320654960631
GO:0040013	negative regulation of locomotion	0.00419320654960631
GO:0050770	regulation of axonogenesis	0.00426732888760441
GO:0048592	eye morphogenesis	0.00426732888760441
GO:0050851	antigen receptor-mediated signaling pathway	0.00430111995345648
GO:0002429	immune response-activating cell surface receptor signaling pathway	0.00464247867992128
GO:0002768	immune response-regulating cell surface receptor signaling pathway	0.00466397163677276
GO:0002757	immune response-activating signal transduction	0.00468430281217282
GO:0002764	immune response-regulating signal transduction	0.00470356392570971
GO:0043010	camera-type eye development	0.00472183728983446
GO:0050767	regulation of neurogenesis	0.00514541387024608
GO:0050870	positive regulation of T cell activation	0.00516430767882716
GO:0051235	maintenance of localization	0.00516430767882716
GO:0005178	integrin binding	0.00516430767882716
GO:0045121	lipid raft	0.00565694624331148
GO:0001654	eye development	0.00565694624331148
GO:0009897	external side of plasma membrane	0.00587718045649609
GO:0051251	positive regulation of lymphocyte activation	0.00587718045649609
GO:0006469	negative regulation of protein kinase activity	0.00624949053066326
GO:0033673	negative regulation of kinase activity	0.00624949053066326
GO:0051348	negative regulation of transferase activity	0.00624949053066326
GO:0050863	regulation of T cell activation	0.00624949053066326
GO:0030334	regulation of cell migration	0.00624949053066326
GO:0051270	regulation of cell motility	0.00681697300413728
GO:0051480	cytosolic calcium ion homeostasis	0.00681697300413728
GO:0007204	elevation of cytosolic calcium ion concentration	0.00681697300413728
GO:0002253	activation of immune response	0.00681697300413728
GO:0040012	regulation of locomotion	0.00681697300413728
GO:0040011	locomotion	0.00681697300413728
GO:0051345	positive regulation of hydrolase activity	0.00683687434010265
GO:0051249	regulation of lymphocyte activation	0.00683687434010265
GO:0051093	negative regulation of developmental process	0.00683687434010265
GO:0050865	regulation of cell activation	0.00698867758267719
GO:0050778	positive regulation of immune response	0.00713956948503045
GO:0007423	sensory organ development	0.00713956948503045
GO:0002684	positive regulation of immune system process	0.00713956948503045
GO:0043086	negative regulation of catalytic activity	0.00713956948503045
GO:0050776	regulation of immune response	0.00770477095470503
GO:0042110	T cell activation	0.00770477095470503
GO:0007160	cell-matrix adhesion	0.00770477095470503
GO:0002682	regulation of immune system process	0.00770477095470503
GO:0032403	protein complex binding	0.00770477095470503
GO:0031589	cell-substrate adhesion	0.00774821094496121
GO:0051240	positive regulation of multicellular organismal process	0.00779046079849803
GO:0007409	axonogenesis	0.00826686993003526
GO:0006874	cellular calcium ion homeostasis	0.00826686993003526
GO:0055074	calcium ion homeostasis	0.00826686993003526
GO:0048667	neuron morphogenesis during differentiation	0.00832249226766375
GO:0048812	neurite morphogenesis	0.00832249226766375
GO:0006875	cellular metal ion homeostasis	0.00832249226766375
GO:0055065	metal ion homeostasis	0.00832249226766375
GO:0000904	cellular morphogenesis during differentiation	0.00832249226766375
GO:0048503	GPI anchor binding	0.00832249226766375
GO:0001525	angiogenesis	0.00841798844973677
GO:0031175	neurite development	0.0087046475248524
GO:0048514	blood vessel morphogenesis	0.00932094556666365
GO:0009986	cell surface	0.00932094556666365
GO:0048646	anatomical structure formation	0.00943275162493369
GO:0048666	neuron development	0.00943275162493369
GO:0046649	lymphocyte activation	0.00943275162493369
GO:0001568	blood vessel development	0.00977275403273284
GO:0005099	Ras GTPase activator activity	0.00977275403273284
GO:0001944	vasculature development	0.00977275403273284
GO:0045321	leukocyte activation	0.0103714949232284
GO:0030005	cellular di-, tri-valent inorganic cation homeostasis	0.0103714949232284
GO:0055066	di-, tri-valent inorganic cation homeostasis	0.0104333599806652
GO:0030003	cellular cation homeostasis	0.0110490992582126
GO:0055080	cation homeostasis	0.0110490992582126
GO:0032990	cell part morphogenesis	0.0110490992582126
GO:0048858	cell projection morphogenesis	0.0110490992582126
GO:0030030	cell projection organization and biogenesis	0.0110490992582126
GO:0001775	cell activation	0.0110953738029834
GO:0030182	neuron differentiation	0.0110953738029834
GO:0043087	regulation of GTPase activity	0.0110953738029834
GO:0016477	cell migration	0.0118856051388725
GO:0050793	regulation of developmental process	0.0118856051388725
GO:0045859	regulation of protein kinase activity	0.0118856051388725
GO:0055082	cellular chemical homeostasis	0.0118856051388725
GO:0006873	cellular ion homeostasis	0.0118856051388725
GO:0048699	generation of neurons	0.0119156952784646
GO:0043549	regulation of kinase activity	0.0119156952784646
GO:0051338	regulation of transferase activity	0.012052320777153
GO:0035091	phosphoinositide binding	0.0121381473818775
GO:0043085	positive regulation of catalytic activity	0.0122703861274615
GO:0022008	neurogenesis	0.0124478156417772
GO:0050801	ion homeostasis	0.0125750618156129
GO:0051239	regulation of multicellular organismal process	0.0129335720694933
GO:0048878	chemical homeostasis	0.013980341779706
GO:0051336	regulation of hydrolase activity	0.014091365371682
GO:0005543	phospholipid binding	0.0152018419518991
GO:0016337	cell-cell adhesion	0.0155772425127937
GO:0005096	GTPase activator activity	0.0155772425127937
GO:0009887	organ morphogenesis	0.0160710942280335
GO:0019725	cellular homeostasis	0.0165128814834598
GO:0006928	cell motility	0.0165953137878253
GO:0051674	localization of cell	0.0165953137878253
GO:0008047	enzyme activator activity	0.0195585907348535
GO:0005083	small GTPase regulator activity	0.0199983696981224
GO:0000902	cell morphogenesis	0.0199983696981224
GO:0032989	cellular structure morphogenesis	0.0199983696981224
GO:0042592	homeostatic process	0.0199983696981224
GO:0005829	cytosol	0.0234840906251489
GO:0008289	lipid binding	0.0237575329415669
GO:0050790	regulation of catalytic activity	0.0246377158013366
GO:0065009	regulation of a molecular function	0.027121545223371
GO:0007010	cytoskeleton organization and biogenesis	0.0275224476802247
GO:0030695	GTPase regulator activity	0.0278776293279587
GO:0007399	nervous system development	0.0283066948220991
GO:0005783	endoplasmic reticulum	0.0355586953962086
GO:0065008	regulation of biological quality	0.0368764263937009
GO:0022610	biological adhesion	0.0368764263937009
GO:0007155	cell adhesion	0.0368764263937009
GO:0005102	receptor binding	0.0395537003961838
GO:0009653	anatomical structure morphogenesis	0.0396558580945723
GO:0048518	positive regulation of biological process	0.0399446603084893
GO:0048523	negative regulation of cellular process	0.042328170338506
GO:0048513	organ development	0.042328170338506
GO:0048519	negative regulation of biological process	0.0435127815911991
GO:0006955	immune response	0.0435127815911991
GO:0048468	cell development	0.0451473262228586
GO:0005887	integral to plasma membrane	0.0480238627889635
GO:0031226	intrinsic to plasma membrane	0.04827972861172
GO:0002376	immune system process	0.049387421219952

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	2.33e-21	76
preadipocyte	5.78e-09	12
skin fibroblast	6.80e-09	23
mesenchymal stem cell of adipose	7.40e-07	8

Uber Anatomy

Ontology term	p-value	n
neural tube	4.12e-14	56
neural rod	4.12e-14	56
future spinal cord	4.12e-14	56
neural keel	4.12e-14	56
regional part of nervous system	6.18e-14	53
regional part of brain	6.18e-14	53
cerebral hemisphere	7.16e-14	32
brain grey matter	3.36e-13	34
gray matter	3.36e-13	34
telencephalon	3.73e-13	34
regional part of telencephalon	9.19e-13	32
regional part of forebrain	1.12e-12	41
forebrain	1.12e-12	41
anterior neural tube	1.12e-12	41
future forebrain	1.12e-12	41
central nervous system	4.95e-12	81
brain	2.31e-11	68
future brain	2.31e-11	68
cerebral cortex	2.37e-11	25
pallium	2.37e-11	25
structure with developmental contribution from neural crest	2.94e-11	132
regional part of cerebral cortex	1.74e-10	22
nervous system	1.11e-09	89
adipose tissue	1.32e-09	14
integument	1.41e-09	46
integumental system	1.41e-09	46
neural plate	1.71e-09	82
presumptive neural plate	1.71e-09	82
neocortex	1.77e-09	20
neurectoderm	6.38e-09	86
surface structure	8.66e-09	99
dense mesenchyme tissue	3.75e-08	73
paraxial mesoderm	1.06e-07	72
presumptive paraxial mesoderm	1.06e-07	72
pre-chordal neural plate	1.23e-07	61
ecto-epithelium	1.84e-07	104
somite	2.18e-07	71
presomitic mesoderm	2.18e-07	71
presumptive segmental plate	2.18e-07	71
dermomyotome	2.18e-07	71
trunk paraxial mesoderm	2.18e-07	71
skin of body	7.50e-07	41
ectoderm-derived structure	7.62e-07	171
ectoderm	7.62e-07	171
presumptive ectoderm	7.62e-07	171

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)
MA0003.1	0.169975
MA0004.1	3.82528
MA0006.1	0.265592
MA0007.1	0.397529
MA0009.1	0.870971
MA0014.1	0.0324647
MA0017.1	0.301634
MA0019.1	0.558663
MA0024.1	0.766783
MA0025.1	1.00397
MA0027.1	2.48103
MA0028.1	0.280275
MA0029.1	0.785955
MA0030.1	0.774581
MA0031.1	0.710608
MA0038.1	0.514558
MA0040.1	0.791764
MA0041.1	0.433167
MA0042.1	0.402577
MA0043.1	0.871285
MA0046.1	0.860127
MA0048.1	0.0764047
MA0050.1	0.403421
MA0051.1	0.510444
MA0052.1	0.795605
MA0055.1	0.0199484
MA0056.1	0
MA0057.1	0.539841
MA0058.1	3.27605
MA0059.1	5.28745
MA0060.1	0.162248
MA0061.1	0.432181
MA0063.1	0
MA0066.1	0.514973
MA0067.1	1.18766
MA0068.1	0.354973
MA0069.1	0.856287
MA0070.1	0.845142
MA0071.1	1.20007
MA0072.1	0.840664
MA0073.1	0.0776172
MA0074.1	0.509711
MA0076.1	0.339975
MA0077.1	0.832987
MA0078.1	0.607575
MA0081.1	0.324031
MA0083.1	0.878452
MA0084.1	1.37471
MA0087.1	0.838229
MA0088.1	1.01254
MA0089.1	0
MA0090.1	0.353576
MA0091.1	0.417885
MA0092.1	0.381858
MA0093.1	2.08959
MA0095.1	0
MA0098.1	0
MA0100.1	0.528088
MA0101.1	0.271368
MA0103.1	0.714036
MA0105.1	0.229733
MA0106.1	1.366
MA0107.1	0.205358
MA0108.2	0.707575
MA0109.1	0
MA0111.1	0.959847
MA0113.1	0.57094
MA0114.1	0.582067
MA0115.1	1.11137
MA0116.1	0.599942
MA0117.1	0.908433
MA0119.1	0.308914
MA0122.1	0.934245
MA0124.1	1.06995
MA0125.1	0.986127
MA0130.1	0
MA0131.1	0.625452
MA0132.1	0
MA0133.1	0
MA0135.1	0.90122
MA0136.1	0.521435
MA0139.1	0.129876
MA0140.1	0.474342
MA0141.1	0.861836
MA0142.1	0.679161
MA0143.1	0.571113
MA0144.1	0.1885
MA0145.1	0.177438
MA0146.1	0.0794051
MA0147.1	1.7891
MA0148.1	1.11902
MA0149.1	1.17441
MA0062.2	0.135498
MA0035.2	0.473658
MA0039.2	0.109483
MA0138.2	0.608783
MA0002.2	0.152495
MA0137.2	0.28622
MA0104.2	1.50683
MA0047.2	0.542971
MA0112.2	3.76262
MA0065.2	0.0483532
MA0150.1	0.34802
MA0151.1	0
MA0152.1	0.480711
MA0153.1	0.969315
MA0154.1	0.488402
MA0155.1	0.0402662
MA0156.1	0.288314
MA0157.1	0.652111
MA0158.1	0
MA0159.1	0.212043
MA0160.1	0.453945
MA0161.1	0
MA0162.1	0.14518
MA0163.1	0.00648562
MA0164.1	0.583138
MA0080.2	0.268439
MA0018.2	0.556211
MA0099.2	0.481058
MA0079.2	0.0127399
MA0102.2	1.41188
MA0258.1	2.29832
MA0259.1	1.82941
MA0442.1	0

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
ESR1#2099	5	17.0936684978636	4.08817970262758e-06	0.000129895162751056

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.