Coexpression cluster:C3184

Full id: C3184_Eosinophils_CD8_CD4_Neutrophils_hairy_Whole_B

Phase1 CAGE Peaks

Hg19::chr11:64107589..64107604,-	p@chr11:64107589..64107604 -
Hg19::chr19:6772686..6772697,+	p2@VAV1
Hg19::chr22:24823517..24823546,+	p5@ADORA2A

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
5.91277682223884e-05	0.0374278772847718	2	220	Signalling by NGF (Reactome):REACT_11061

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:0006909	phagocytosis	0.00025294983684129
GO:0010324	membrane invagination	0.00198514209351949
GO:0006897	endocytosis	0.00198514209351949
GO:0032230	positive regulation of synaptic transmission, GABAergic	0.00247927857153759
GO:0016044	membrane organization and biogenesis	0.00247927857153759
GO:0001973	adenosine receptor signaling pathway	0.00299401826913486
GO:0001611	A2A adenosine receptor activity, G-protein coupled	0.00299401826913486
GO:0032228	regulation of synaptic transmission, GABAergic	0.00349291848885374
GO:0042755	eating behavior	0.00349291848885374
GO:0051932	synaptic transmission, GABAergic	0.00349291848885374
GO:0001975	response to amphetamine	0.00349291848885374
GO:0014075	response to amine stimulus	0.00349291848885374
GO:0050790	regulation of catalytic activity	0.00366740246370577
GO:0016192	vesicle-mediated transport	0.00366740246370577
GO:0050806	positive regulation of synaptic transmission	0.00366740246370577
GO:0065009	regulation of a molecular function	0.00366740246370577
GO:0001609	adenosine receptor activity, G-protein coupled	0.00366740246370577
GO:0030676	Rac guanyl-nucleotide exchange factor activity	0.00366740246370577
GO:0051971	positive regulation of transmission of nerve impulse	0.00366740246370577
GO:0001963	synaptic transmission, dopaminergic	0.00366740246370577
GO:0031646	positive regulation of neurological process	0.00399167181551987
GO:0045785	positive regulation of cell adhesion	0.00714344921713767
GO:0050804	regulation of synaptic transmission	0.00728828147067584
GO:0051969	regulation of transmission of nerve impulse	0.00765586138917796
GO:0007270	nerve-nerve synaptic transmission	0.00765586138917796
GO:0006171	cAMP biosynthetic process	0.00765586138917796
GO:0046058	cAMP metabolic process	0.00851123181759712
GO:0007190	adenylate cyclase activation	0.00851123181759712
GO:0031644	regulation of neurological process	0.00851123181759712
GO:0045762	positive regulation of adenylate cyclase activity	0.00851123181759712
GO:0031281	positive regulation of cyclase activity	0.00851123181759712
GO:0051349	positive regulation of lyase activity	0.00851123181759712
GO:0007189	G-protein signaling, adenylate cyclase activating pathway	0.0109712805277906
GO:0007631	feeding behavior	0.0109712805277906
GO:0009190	cyclic nucleotide biosynthetic process	0.0109712805277906
GO:0045761	regulation of adenylate cyclase activity	0.0109712805277906
GO:0031279	regulation of cyclase activity	0.0109712805277906
GO:0051339	regulation of lyase activity	0.0109712805277906
GO:0045028	purinergic nucleotide receptor activity, G-protein coupled	0.0109712805277906
GO:0001608	nucleotide receptor activity, G-protein coupled	0.0109712805277906
GO:0016502	nucleotide receptor activity	0.0109712805277906
GO:0001614	purinergic nucleotide receptor activity	0.0109712805277906
GO:0009187	cyclic nucleotide metabolic process	0.0121763494559456
GO:0007242	intracellular signaling cascade	0.0135282592478952
GO:0019992	diacylglycerol binding	0.0137276904705138
GO:0010033	response to organic substance	0.0141114826117002
GO:0030155	regulation of cell adhesion	0.0147014195766507
GO:0006968	cellular defense response	0.0157024009538919
GO:0007188	G-protein signaling, coupled to cAMP nucleotide second messenger	0.0175506373098121
GO:0007229	integrin-mediated signaling pathway	0.0175506373098121
GO:0019933	cAMP-mediated signaling	0.0175506373098121
GO:0007166	cell surface receptor linked signal transduction	0.0175506373098121
GO:0007596	blood coagulation	0.0197432993336674
GO:0050817	coagulation	0.019764653657151
GO:0007599	hemostasis	0.0199751569658774
GO:0007187	G-protein signaling, coupled to cyclic nucleotide second messenger	0.0218567002300837
GO:0019935	cyclic-nucleotide-mediated signaling	0.0223892589633975
GO:0050878	regulation of body fluid levels	0.0225433032418296
GO:0042060	wound healing	0.0232228968375412
GO:0005089	Rho guanyl-nucleotide exchange factor activity	0.0262997025568311
GO:0016043	cellular component organization and biogenesis	0.0262997025568311
GO:0008015	blood circulation	0.0262997025568311
GO:0003013	circulatory system process	0.0262997025568311
GO:0035023	regulation of Rho protein signal transduction	0.0262997025568311
GO:0005088	Ras guanyl-nucleotide exchange factor activity	0.0265368819590599
GO:0007626	locomotory behavior	0.0286623246375753
GO:0007266	Rho protein signal transduction	0.0293234423434123
GO:0043087	regulation of GTPase activity	0.0324158935762655
GO:0007417	central nervous system development	0.0355671701565904
GO:0006810	transport	0.0358650919401976
GO:0051234	establishment of localization	0.0366111125560204
GO:0009165	nucleotide biosynthetic process	0.0366111125560204
GO:0043085	positive regulation of catalytic activity	0.0366111125560204
GO:0019932	second-messenger-mediated signaling	0.0378026194446836
GO:0051239	regulation of multicellular organismal process	0.0385460220629078
GO:0007268	synaptic transmission	0.039193714268358
GO:0006954	inflammatory response	0.039193714268358
GO:0007610	behavior	0.039193714268358
GO:0051179	localization	0.039193714268358
GO:0051336	regulation of hydrolase activity	0.0397950531681832
GO:0005085	guanyl-nucleotide exchange factor activity	0.0397950531681832
GO:0019226	transmission of nerve impulse	0.0419682489221858
GO:0009117	nucleotide metabolic process	0.0427127318453849
GO:0055086	nucleobase, nucleoside and nucleotide metabolic process	0.0455375661295008
GO:0046578	regulation of Ras protein signal transduction	0.0458554250684929
GO:0007165	signal transduction	0.0474101992469932

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
leukocyte	1.88e-80	136
hematopoietic stem cell	7.17e-74	168
angioblastic mesenchymal cell	7.17e-74	168
hematopoietic cell	8.65e-73	177
hematopoietic oligopotent progenitor cell	6.50e-67	161
hematopoietic multipotent progenitor cell	6.50e-67	161
nongranular leukocyte	7.77e-65	115
hematopoietic lineage restricted progenitor cell	3.96e-60	120
lymphocyte	9.61e-55	53
common lymphoid progenitor	9.61e-55	53
lymphoid lineage restricted progenitor cell	6.36e-54	52
nucleate cell	5.23e-52	55
T cell	8.81e-28	25
pro-T cell	8.81e-28	25
lymphocyte of B lineage	1.47e-23	24
pro-B cell	1.47e-23	24
mature alpha-beta T cell	5.39e-21	18
alpha-beta T cell	5.39e-21	18
immature T cell	5.39e-21	18
mature T cell	5.39e-21	18
immature alpha-beta T cell	5.39e-21	18
myeloid leukocyte	1.12e-20	72
myeloid cell	5.67e-20	108
common myeloid progenitor	5.67e-20	108
mesenchymal cell	5.01e-16	354
classical monocyte	8.10e-16	42
CD14-positive, CD16-negative classical monocyte	8.10e-16	42
connective tissue cell	4.35e-15	361
granulocyte monocyte progenitor cell	3.20e-14	67
CD8-positive, alpha-beta T cell	5.21e-14	11
macrophage dendritic cell progenitor	6.97e-14	61
defensive cell	1.22e-13	48
phagocyte	1.22e-13	48
monopoietic cell	1.24e-13	59
monocyte	1.24e-13	59
monoblast	1.24e-13	59
promonocyte	1.24e-13	59
myeloid lineage restricted progenitor cell	1.39e-13	66
B cell	2.55e-13	14
motile cell	7.42e-12	386
granulocyte	5.03e-10	8
blood cell	3.14e-08	11
multi fate stem cell	4.09e-08	427
CD4-positive, alpha-beta T cell	1.04e-07	6
somatic stem cell	1.27e-07	433
intermediate monocyte	1.69e-07	9
CD14-positive, CD16-positive monocyte	1.69e-07	9
stem cell	2.37e-07	441

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	6.60e-28	98
blood island	6.60e-28	98
hemolymphoid system	1.18e-24	108
immune system	3.68e-15	93
connective tissue	8.02e-14	371
blood	9.07e-14	15
haemolymphatic fluid	9.07e-14	15
organism substance	9.07e-14	15
bone marrow	8.24e-13	76
bone element	4.80e-11	82
skeletal element	4.19e-09	90
hemopoietic organ	1.43e-08	7
immune organ	1.43e-08	7
skeletal system	3.48e-07	100

Disease

Ontology term	p-value	n
lymphoma	1.52e-10	10
hematologic cancer	1.13e-09	51
immune system cancer	1.13e-09	51

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	0.401049
MA0004.1	0.826076
MA0006.1	0.639288
MA0007.1	0.804807
MA0009.1	1.3275
MA0014.1	0.758317
MA0017.1	0.686276
MA0019.1	0.990656
MA0024.1	1.21731
MA0025.1	1.46617
MA0027.1	2.95767
MA0028.1	0.658629
MA0029.1	1.23771
MA0030.1	1.22561
MA0031.1	1.15713
MA0038.1	0.94098
MA0040.1	1.24388
MA0041.1	0.847069
MA0042.1	0.810843
MA0043.1	1.32783
MA0046.1	1.31611
MA0048.1	1.62115
MA0050.1	0.81185
MA0051.1	0.936307
MA0052.1	1.24796
MA0055.1	0.557638
MA0056.1	0
MA0057.1	1.59304
MA0058.1	0.716037
MA0059.1	0.714521
MA0060.1	0.492218
MA0061.1	1.15625
MA0063.1	0
MA0066.1	2.1667
MA0067.1	1.65513
MA0068.1	0.405474
MA0069.1	1.31207
MA0070.1	1.30033
MA0071.1	0.897953
MA0072.1	1.29561
MA0073.1	5.1975
MA0074.1	0.935474
MA0076.1	0.734647
MA0077.1	1.28751
MA0078.1	1.04495
MA0081.1	1.70054
MA0083.1	1.33535
MA0084.1	1.84562
MA0087.1	1.29304
MA0088.1	0.257905
MA0089.1	0
MA0090.1	0.751469
MA0091.1	0.829044
MA0092.1	0.785956
MA0093.1	1.55117
MA0095.1	0
MA0098.1	0
MA0100.1	0.956299
MA0101.1	0.646932
MA0103.1	1.52002
MA0105.1	0.846801
MA0106.1	0.986396
MA0107.1	0.556367
MA0108.2	1.15387
MA0109.1	0
MA0111.1	0.767139
MA0113.1	1.00436
MA0114.1	0.549955
MA0115.1	1.57693
MA0116.1	0.560723
MA0117.1	1.36676
MA0119.1	0.695578
MA0122.1	1.39371
MA0124.1	1.53432
MA0125.1	1.44766
MA0130.1	0
MA0131.1	1.06461
MA0132.1	0
MA0133.1	0
MA0135.1	1.35921
MA0136.1	0.948776
MA0139.1	0.440097
MA0140.1	0.894983
MA0141.1	0.712476
MA0142.1	1.12317
MA0143.1	1.00455
MA0144.1	0.531867
MA0145.1	0.273764
MA0146.1	0.707589
MA0147.1	0.565108
MA0148.1	0.854239
MA0149.1	0.884158
MA0062.2	0.449458
MA0035.2	0.894194
MA0039.2	0.757898
MA0138.2	1.04628
MA0002.2	1.20011
MA0137.2	0.666381
MA0104.2	0.491226
MA0047.2	0.973066
MA0112.2	3.77966
MA0065.2	1.39232
MA0150.1	0.744617
MA0151.1	0
MA0152.1	0.902317
MA0153.1	1.43021
MA0154.1	0.312019
MA0155.1	2.02721
MA0156.1	0.669101
MA0157.1	1.09377
MA0158.1	0
MA0159.1	0.565904
MA0160.1	0.871361
MA0161.1	0
MA0162.1	0.455568
MA0163.1	2.48891
MA0164.1	1.01792
MA0080.2	1.55139
MA0018.2	0.987913
MA0099.2	0.902716
MA0079.2	2.70224
MA0102.2	1.88331
MA0258.1	2.22591
MA0259.1	0.575594
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
EBF1#1879	3	8.906466846569	0.0014152328356098	0.0091260497726755
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460265034437471
ZEB1#6935	2	11.2589546783626	0.0101022267664633	0.0377983900427277

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.