Coexpression cluster:C1444

Full id: C1444_immature_migratory_CD14_amniotic_Eosinophils_CD19_Neutrophils

Phase1 CAGE Peaks

Hg19::chr18:56338727..56338743,+	p3@MALT1
Hg19::chr1:11863148..11863162,-	p15@MTHFR
Hg19::chr1:11863171..11863195,-	p7@MTHFR
Hg19::chr2:65593835..65593877,-	p4@SPRED2
Hg19::chr4:100737954..100738014,+	p1@DAPP1
Hg19::chr4:100738030..100738037,+	p3@DAPP1

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
4.07274183298443e-05	0.0257804558027915	2	75	B cell receptor signaling pathway (KEGG):04662

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:0019207	kinase regulator activity	0.00913554713606416
GO:0045859	regulation of protein kinase activity	0.00913554713606416
GO:0043549	regulation of kinase activity	0.00913554713606416
GO:0051338	regulation of transferase activity	0.00913554713606416
GO:0004489	methylenetetrahydrofolate reductase (NADPH) activity	0.00913554713606416
GO:0032449	CBM complex	0.00913554713606416
GO:0002711	positive regulation of T cell mediated immunity	0.00913554713606416
GO:0032743	positive regulation of interleukin-2 production	0.00913554713606416
GO:0002726	positive regulation of T cell cytokine production	0.00913554713606416
GO:0002369	T cell cytokine production	0.00913554713606416
GO:0002724	regulation of T cell cytokine production	0.00913554713606416
GO:0002702	positive regulation of production of molecular mediator of immune response	0.00913554713606416
GO:0002720	positive regulation of cytokine production during immune response	0.00913554713606416
GO:0005173	stem cell factor receptor binding	0.00913554713606416
GO:0002709	regulation of T cell mediated immunity	0.00913554713606416
GO:0032663	regulation of interleukin-2 production	0.00913554713606416
GO:0007243	protein kinase cascade	0.00913554713606416
GO:0002824	positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.00937218767921216
GO:0002718	regulation of cytokine production during immune response	0.00937218767921216
GO:0002821	positive regulation of adaptive immune response	0.00937218767921216
GO:0002700	regulation of production of molecular mediator of immune response	0.00937218767921216
GO:0002367	cytokine production during immune response	0.00937218767921216
GO:0035014	phosphoinositide 3-kinase regulator activity	0.00937218767921216
GO:0043621	protein self-association	0.00937218767921216
GO:0002705	positive regulation of leukocyte mediated immunity	0.00937218767921216
GO:0002456	T cell mediated immunity	0.00937218767921216
GO:0002708	positive regulation of lymphocyte mediated immunity	0.00937218767921216
GO:0002699	positive regulation of immune effector process	0.00967412384808736
GO:0007250	activation of NF-kappaB-inducing kinase	0.00967412384808736
GO:0002703	regulation of leukocyte mediated immunity	0.00967412384808736
GO:0002706	regulation of lymphocyte mediated immunity	0.00967412384808736
GO:0009086	methionine biosynthetic process	0.00967412384808736
GO:0002819	regulation of adaptive immune response	0.00967412384808736
GO:0002822	regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains.	0.00967412384808736
GO:0002697	regulation of immune effector process	0.0108425657983243
GO:0050790	regulation of catalytic activity	0.0110794343074728
GO:0009067	aspartate family amino acid biosynthetic process	0.0111055472779436
GO:0050852	T cell receptor signaling pathway	0.0111055472779436
GO:0006555	methionine metabolic process	0.0111055472779436
GO:0019209	kinase activator activity	0.0111055472779436
GO:0000188	inactivation of MAPK activity	0.0111055472779436
GO:0065009	regulation of a molecular function	0.0114971521612877
GO:0005942	phosphoinositide 3-kinase complex	0.0114971521612877
GO:0000097	sulfur amino acid biosynthetic process	0.0114971521612877
GO:0032623	interleukin-2 production	0.0118032216391385
GO:0001819	positive regulation of cytokine production	0.0126451920081803
GO:0043407	negative regulation of MAP kinase activity	0.0129136683529758
GO:0002440	production of molecular mediator of immune response	0.0138461843222623
GO:0050851	antigen receptor-mediated signaling pathway	0.0138461843222623
GO:0009966	regulation of signal transduction	0.0138461843222623
GO:0009066	aspartate family amino acid metabolic process	0.0138818511611803
GO:0000096	sulfur amino acid metabolic process	0.0141005159226811
GO:0002429	immune response-activating cell surface receptor signaling pathway	0.0143108870724969
GO:0002768	immune response-regulating cell surface receptor signaling pathway	0.0145134253692679
GO:0002757	immune response-activating signal transduction	0.0147085580619147
GO:0002764	immune response-regulating signal transduction	0.014896681881578
GO:0016646	oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor	0.0150781657186168
GO:0050870	positive regulation of T cell activation	0.0175607085218321
GO:0001817	regulation of cytokine production	0.0175607085218321
GO:0005515	protein binding	0.0176817365756131
GO:0051168	nuclear export	0.0180470171372814
GO:0032501	multicellular organismal process	0.0180470171372814
GO:0044272	sulfur compound biosynthetic process	0.0180470171372814
GO:0030693	caspase activity	0.0197345665058968
GO:0051251	positive regulation of lymphocyte activation	0.0198187015967892
GO:0016645	oxidoreductase activity, acting on the CH-NH group of donors	0.019900253366686
GO:0006469	negative regulation of protein kinase activity	0.0211674835851774
GO:0033673	negative regulation of kinase activity	0.0211674835851774
GO:0051348	negative regulation of transferase activity	0.021282316428579
GO:0050863	regulation of T cell activation	0.021282316428579
GO:0051259	protein oligomerization	0.0220465540844657
GO:0032147	activation of protein kinase activity	0.0245368867182962
GO:0002253	activation of immune response	0.0245454059728686
GO:0002449	lymphocyte mediated immunity	0.0245536648911535
GO:0002250	adaptive immune response	0.0249035740846093
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0249035740846093
GO:0051249	regulation of lymphocyte activation	0.0249035740846093
GO:0002443	leukocyte mediated immunity	0.0252290237302291
GO:0050865	regulation of cell activation	0.0255461214629594
GO:0008652	amino acid biosynthetic process	0.0261196739881982
GO:0050778	positive regulation of immune response	0.0261196739881982
GO:0006790	sulfur metabolic process	0.0261196739881982
GO:0002684	positive regulation of immune system process	0.0261196739881982
GO:0043086	negative regulation of catalytic activity	0.0261196739881982
GO:0043405	regulation of MAP kinase activity	0.027585235601085
GO:0050776	regulation of immune response	0.0283196817116856
GO:0042110	T cell activation	0.0283196817116856
GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB cascade	0.0283196817116856
GO:0002682	regulation of immune system process	0.0283196817116856
GO:0007165	signal transduction	0.0290757114283303
GO:0051240	positive regulation of multicellular organismal process	0.0290757114283303
GO:0043122	regulation of I-kappaB kinase/NF-kappaB cascade	0.0295774556148059
GO:0002252	immune effector process	0.0297986264495236
GO:0001816	cytokine production	0.0302816501657053
GO:0009309	amine biosynthetic process	0.0315454828143631
GO:0007154	cell communication	0.0344384781344397
GO:0007249	I-kappaB kinase/NF-kappaB cascade	0.0360556320903252
GO:0045860	positive regulation of protein kinase activity	0.0360849101192422
GO:0004197	cysteine-type endopeptidase activity	0.0360849101192422
GO:0033674	positive regulation of kinase activity	0.0362240154231583
GO:0044271	nitrogen compound biosynthetic process	0.0362488046806512
GO:0051347	positive regulation of transferase activity	0.0362488046806512
GO:0000165	MAPKKK cascade	0.0365640539599067
GO:0009967	positive regulation of signal transduction	0.0365640539599067
GO:0006913	nucleocytoplasmic transport	0.0365640539599067
GO:0046649	lymphocyte activation	0.0365640539599067
GO:0051169	nuclear transport	0.0365640539599067
GO:0007242	intracellular signaling cascade	0.0365640539599067
GO:0008015	blood circulation	0.0365640539599067
GO:0003013	circulatory system process	0.0365640539599067
GO:0004842	ubiquitin-protein ligase activity	0.0371339497738497
GO:0008639	small protein conjugating enzyme activity	0.037247914142536
GO:0006916	anti-apoptosis	0.0378012012049799
GO:0045321	leukocyte activation	0.0396561771719475
GO:0044445	cytosolic part	0.0414769691378795
GO:0043687	post-translational protein modification	0.0440000489858293
GO:0001775	cell activation	0.0448071134385577
GO:0004725	protein tyrosine phosphatase activity	0.0463221020896512
GO:0043066	negative regulation of apoptosis	0.0478101264284914
GO:0043069	negative regulation of programmed cell death	0.0480319249969728
GO:0019787	small conjugating protein ligase activity	0.049888895594376

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
leukocyte	5.61e-33	136
nongranular leukocyte	1.11e-31	115
hematopoietic lineage restricted progenitor cell	4.58e-29	120
classical monocyte	4.36e-26	42
CD14-positive, CD16-negative classical monocyte	4.36e-26	42
macrophage dendritic cell progenitor	3.48e-25	61
hematopoietic stem cell	3.26e-24	168
angioblastic mesenchymal cell	3.26e-24	168
hematopoietic cell	4.09e-24	177
monopoietic cell	1.01e-23	59
monocyte	1.01e-23	59
monoblast	1.01e-23	59
promonocyte	1.01e-23	59
defensive cell	1.40e-23	48
phagocyte	1.40e-23	48
granulocyte monocyte progenitor cell	6.34e-23	67
hematopoietic oligopotent progenitor cell	4.17e-22	161
hematopoietic multipotent progenitor cell	4.17e-22	161
myeloid lineage restricted progenitor cell	5.16e-21	66
myeloid leukocyte	6.29e-20	72
myeloid cell	7.80e-14	108
common myeloid progenitor	7.80e-14	108
lymphocyte of B lineage	2.43e-11	24
pro-B cell	2.43e-11	24
lymphocyte	3.00e-08	53
common lymphoid progenitor	3.00e-08	53
lymphoid lineage restricted progenitor cell	7.98e-08	52
nucleate cell	1.02e-07	55
B cell	1.51e-07	14
dendritic cell	1.72e-07	10
endo-epithelial cell	3.76e-07	42

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	3.15e-22	98
blood island	3.15e-22	98
bone marrow	2.68e-18	76
hemolymphoid system	2.41e-17	108
bone element	3.82e-15	82
immune system	4.31e-15	93
skeletal element	6.10e-15	90
skeletal system	4.37e-13	100

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
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0380309803622546
SRF#6722	5	11.4976485518065	1.12681431027194e-05	0.000288157100270546
TCF12#6938	3	5.31723245109321	0.01336734573386	0.0472476046127861
TFAP2C#7022	3	5.40461430493011	0.0127757616669587	0.0460639291837155

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.