Coexpression cluster:C537

Full id: C537_immature_CD14_migratory_Mast_CD4_Dendritic_Basophils

Phase1 CAGE Peaks

Hg19::chr12:100967533..100967548,+	p3@GAS2L3
Hg19::chr13:99948360..99948387,-	p5@GPR183
Hg19::chr13:99959641..99959660,-	p1@GPR183
Hg19::chr16:11670817..11670855,-	p@chr16:11670817..11670855 -
Hg19::chr18:56338201..56338239,+	p8@MALT1
Hg19::chr18:56338750..56338823,+	p2@MALT1
Hg19::chr1:192544895..192544912,+	p1@RGS1
Hg19::chr1:192545731..192545733,+	p@chr1:192545731..192545733 +
Hg19::chr1:192548520..192548535,+	p@chr1:192548520..192548535 +
Hg19::chr1:192548540..192548575,+	p@chr1:192548540..192548575 +
Hg19::chr1:192578548..192578577,+	p@chr1:192578548..192578577 +
Hg19::chr1:206756466..206756481,+	p15@RASSF5
Hg19::chr1:206756498..206756508,+	p13@RASSF5
Hg19::chr2:201997492..201997510,+	p22@CFLAR
Hg19::chr6:134495992..134496010,-	p1@SGK1
Hg19::chr7:6066589..6066602,-	p4@EIF2AK1
Hg19::chr9:134505871..134505884,-	p@chr9:134505871..134505884 -

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:0048523	negative regulation of cellular process	2.24315862494925e-07
GO:0048519	negative regulation of biological process	2.24315862494925e-07
GO:0050794	regulation of cellular process	0.0017810822156576
GO:0030693	caspase activity	0.0017810822156576
GO:0050789	regulation of biological process	0.0017810822156576
GO:0065007	biological regulation	0.00257669638261057
GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB cascade	0.00376780878370422
GO:0043122	regulation of I-kappaB kinase/NF-kappaB cascade	0.00376780878370422
GO:0007242	intracellular signaling cascade	0.00376780878370422
GO:0046984	regulation of hemoglobin biosynthetic process	0.00376780878370422
GO:0046986	negative regulation of hemoglobin biosynthetic process	0.00376780878370422
GO:0045993	negative regulation of translational initiation by iron	0.00376780878370422
GO:0007249	I-kappaB kinase/NF-kappaB cascade	0.0042882600480954
GO:0009966	regulation of signal transduction	0.0042882600480954
GO:0004197	cysteine-type endopeptidase activity	0.0042882600480954
GO:0009967	positive regulation of signal transduction	0.0042882600480954
GO:0006915	apoptosis	0.0042882600480954
GO:0012501	programmed cell death	0.0042882600480954
GO:0006447	regulation of translational initiation by iron	0.0042882600480954
GO:0016265	death	0.0042882600480954
GO:0008219	cell death	0.0042882600480954
GO:0006916	anti-apoptosis	0.0042882600480954
GO:0032449	CBM complex	0.00583273858869478
GO:0045786	negative regulation of progression through cell cycle	0.00583273858869478
GO:0043066	negative regulation of apoptosis	0.00583273858869478
GO:0043069	negative regulation of programmed cell death	0.00583273858869478
GO:0004694	eukaryotic translation initiation factor 2alpha kinase activity	0.00583273858869478
GO:0042541	hemoglobin biosynthetic process	0.00583273858869478
GO:0002711	positive regulation of T cell mediated immunity	0.00583273858869478
GO:0002726	positive regulation of T cell cytokine production	0.00583273858869478
GO:0032743	positive regulation of interleukin-2 production	0.00583273858869478
GO:0002369	T cell cytokine production	0.00656329538340829
GO:0020027	hemoglobin metabolic process	0.00656329538340829
GO:0002724	regulation of T cell cytokine production	0.00656329538340829
GO:0048468	cell development	0.00656329538340829
GO:0002720	positive regulation of cytokine production during immune response	0.00695339556003099
GO:0002709	regulation of T cell mediated immunity	0.00695339556003099
GO:0002702	positive regulation of production of molecular mediator of immune response	0.00695339556003099
GO:0032663	regulation of interleukin-2 production	0.00695339556003099
GO:0008234	cysteine-type peptidase activity	0.00724077483814711
GO:0000074	regulation of progression through cell cycle	0.00859537530791841
GO:0002824	positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.00859537530791841
GO:0002718	regulation of cytokine production during immune response	0.00859537530791841
GO:0002700	regulation of production of molecular mediator of immune response	0.00859537530791841
GO:0002821	positive regulation of adaptive immune response	0.00859537530791841
GO:0002367	cytokine production during immune response	0.00859537530791841
GO:0045947	negative regulation of translational initiation	0.00859537530791841
GO:0051726	regulation of cell cycle	0.00859537530791841
GO:0043621	protein self-association	0.00859537530791841
GO:0002705	positive regulation of leukocyte mediated immunity	0.00859537530791841
GO:0002456	T cell mediated immunity	0.00859537530791841
GO:0002708	positive regulation of lymphocyte mediated immunity	0.00859537530791841
GO:0007243	protein kinase cascade	0.00859537530791841
GO:0002699	positive regulation of immune effector process	0.00920342365642115
GO:0007250	activation of NF-kappaB-inducing kinase	0.0095109723453188
GO:0002703	regulation of leukocyte mediated immunity	0.0095109723453188
GO:0002706	regulation of lymphocyte mediated immunity	0.0095109723453188
GO:0002819	regulation of adaptive immune response	0.00995354786076241
GO:0002822	regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains.	0.00995354786076241
GO:0008047	enzyme activator activity	0.0108648337132161
GO:0002697	regulation of immune effector process	0.0108648337132161
GO:0048869	cellular developmental process	0.0108648337132161
GO:0030154	cell differentiation	0.0108648337132161
GO:0050852	T cell receptor signaling pathway	0.0119957574765944
GO:0007193	G-protein signaling, adenylate cyclase inhibiting pathway	0.012315593328365
GO:0019209	kinase activator activity	0.012315593328365
GO:0032623	interleukin-2 production	0.0141506172788111
GO:0042981	regulation of apoptosis	0.015046854486826
GO:0001819	positive regulation of cytokine production	0.015046854486826
GO:0043067	regulation of programmed cell death	0.0150471991741007
GO:0002440	production of molecular mediator of immune response	0.0169227294353164
GO:0050851	antigen receptor-mediated signaling pathway	0.0169227294353164
GO:0022402	cell cycle process	0.0169247527158631
GO:0002429	immune response-activating cell surface receptor signaling pathway	0.0182908043949664
GO:0002768	immune response-regulating cell surface receptor signaling pathway	0.0186471190494062
GO:0002757	immune response-activating signal transduction	0.0189939697488288
GO:0002764	immune response-regulating signal transduction	0.019331725228904
GO:0008624	induction of apoptosis by extracellular signals	0.0195617293708246
GO:0007165	signal transduction	0.0195617293708246
GO:0005515	protein binding	0.0195617293708246
GO:0065003	macromolecular complex assembly	0.0220037306241794
GO:0017148	negative regulation of translation	0.0220037306241794
GO:0050870	positive regulation of T cell activation	0.0220037306241794
GO:0001817	regulation of cytokine production	0.0220037306241794
GO:0046777	protein amino acid autophosphorylation	0.0228721929696117
GO:0051168	nuclear export	0.0228721929696117
GO:0004175	endopeptidase activity	0.0228721929696117
GO:0031327	negative regulation of cellular biosynthetic process	0.0228721929696117
GO:0022607	cellular component assembly	0.0228721929696117
GO:0016540	protein autoprocessing	0.0228721929696117
GO:0007154	cell communication	0.0228721929696117
GO:0007049	cell cycle	0.0238033305506717
GO:0051251	positive regulation of lymphocyte activation	0.0244407496816509
GO:0009890	negative regulation of biosynthetic process	0.0244407496816509
GO:0006446	regulation of translational initiation	0.0265446408743006
GO:0019992	diacylglycerol binding	0.0273839977685522
GO:0050863	regulation of T cell activation	0.0273839977685522
GO:0051259	protein oligomerization	0.0283440663215144
GO:0048522	positive regulation of cellular process	0.0283440663215144
GO:0032147	activation of protein kinase activity	0.031489309870482
GO:0002253	activation of immune response	0.0316206014706882
GO:0002449	lymphocyte mediated immunity	0.0317492540192714
GO:0002250	adaptive immune response	0.0325284149901371
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0325284149901371
GO:0051249	regulation of lymphocyte activation	0.0325284149901371
GO:0048518	positive regulation of biological process	0.0325284149901371
GO:0002443	leukocyte mediated immunity	0.0327733114089864
GO:0050865	regulation of cell activation	0.0332975156710067
GO:0007188	G-protein signaling, coupled to cAMP nucleotide second messenger	0.0345909721499402
GO:0050778	positive regulation of immune response	0.0345909721499402
GO:0002684	positive regulation of immune system process	0.0345909721499402
GO:0032502	developmental process	0.0345909721499402
GO:0019933	cAMP-mediated signaling	0.0345909721499402
GO:0006955	immune response	0.0375347261122997
GO:0042110	T cell activation	0.0376609939647763
GO:0050776	regulation of immune response	0.0376609939647763
GO:0006413	translational initiation	0.0376609939647763
GO:0016485	protein processing	0.0376609939647763
GO:0002682	regulation of immune system process	0.0377189576754196
GO:0007050	cell cycle arrest	0.0377759005116457
GO:0008233	peptidase activity	0.0379408528307297
GO:0051248	negative regulation of protein metabolic process	0.0379408528307297
GO:0009968	negative regulation of signal transduction	0.0379408528307297
GO:0051240	positive regulation of multicellular organismal process	0.0379939572091468
GO:0002252	immune effector process	0.0394702486707968
GO:0001816	cytokine production	0.0402160355131639
GO:0004871	signal transducer activity	0.0402866767778344
GO:0060089	molecular transducer activity	0.0402866767778344
GO:0006508	proteolysis	0.0402866767778344
GO:0007187	G-protein signaling, coupled to cyclic nucleotide second messenger	0.0403465209399871
GO:0019935	cyclic-nucleotide-mediated signaling	0.0414180612908684
GO:0019207	kinase regulator activity	0.0414180612908684
GO:0002376	immune system process	0.0430407520909788
GO:0022618	protein-RNA complex assembly	0.046395642167172
GO:0045860	positive regulation of protein kinase activity	0.046395642167172
GO:0005516	calmodulin binding	0.046395642167172
GO:0033674	positive regulation of kinase activity	0.0470265471912302
GO:0051347	positive regulation of transferase activity	0.0476478819210036
GO:0006913	nucleocytoplasmic transport	0.0494565020587583
GO:0046649	lymphocyte activation	0.0494565020587583
GO:0051169	nuclear transport	0.0494565020587583
GO:0042803	protein homodimerization activity	0.0497304947002505

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
myeloid leukocyte	4.13e-89	72
leukocyte	1.73e-87	136
granulocyte monocyte progenitor cell	7.30e-87	67
macrophage dendritic cell progenitor	4.73e-86	61
classical monocyte	2.23e-83	42
CD14-positive, CD16-negative classical monocyte	2.23e-83	42
defensive cell	2.19e-82	48
phagocyte	2.19e-82	48
monopoietic cell	1.18e-81	59
monocyte	1.18e-81	59
monoblast	1.18e-81	59
promonocyte	1.18e-81	59
myeloid lineage restricted progenitor cell	5.08e-81	66
hematopoietic lineage restricted progenitor cell	2.58e-68	120
nongranular leukocyte	7.98e-67	115
hematopoietic stem cell	9.45e-67	168
angioblastic mesenchymal cell	9.45e-67	168
myeloid cell	2.05e-65	108
common myeloid progenitor	2.05e-65	108
hematopoietic cell	2.91e-62	177
hematopoietic oligopotent progenitor cell	1.30e-60	161
hematopoietic multipotent progenitor cell	1.30e-60	161
stuff accumulating cell	6.11e-39	87
dendritic cell	1.95e-20	10
mesenchymal cell	2.27e-20	354
connective tissue cell	1.46e-19	361
intermediate monocyte	2.17e-17	9
CD14-positive, CD16-positive monocyte	2.17e-17	9
conventional dendritic cell	3.64e-17	8
motile cell	9.91e-17	386
multi fate stem cell	2.70e-13	427
stem cell	7.35e-13	441
somatic stem cell	8.00e-13	433
immature conventional dendritic cell	3.92e-12	5
common dendritic progenitor	3.92e-12	5
Langerhans cell	6.28e-11	5
basophil	5.62e-07	3
single nucleate cell	9.50e-07	3
mononuclear cell	9.50e-07	3

Uber Anatomy

Ontology term	p-value	n
bone marrow	1.14e-74	76
hematopoietic system	2.07e-72	98
blood island	2.07e-72	98
immune system	1.34e-71	93
bone element	5.17e-68	82
hemolymphoid system	3.98e-66	108
skeletal element	1.64e-60	90
skeletal system	8.18e-53	100
musculoskeletal system	3.56e-26	167
lateral plate mesoderm	1.29e-25	203
connective tissue	3.23e-19	371
mesoderm	1.25e-11	315
mesoderm-derived structure	1.25e-11	315
presumptive mesoderm	1.25e-11	315

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	0.196975
MA0004.1	0.631966
MA0006.1	0.362024
MA0007.1	0.208008
MA0009.1	0.621697
MA0014.1	0.0424137
MA0017.1	0.425352
MA0019.1	0.340029
MA0024.1	0.525161
MA0025.1	0.747404
MA0027.1	2.20546
MA0028.1	0.122394
MA0029.1	0.542771
MA0030.1	0.532314
MA0031.1	0.474026
MA0038.1	0.302644
MA0040.1	0.548121
MA0041.1	1.2374
MA0042.1	0.608306
MA0043.1	0.621991
MA0046.1	0.611559
MA0048.1	0.0663643
MA0050.1	0.212584
MA0051.1	0.299199
MA0052.1	0.551663
MA0055.1	0.0307766
MA0056.1	0
MA0057.1	0.0128587
MA0058.1	0.467197
MA0059.1	0.15289
MA0060.1	0.18988
MA0061.1	0.0397345
MA0063.1	0
MA0066.1	0.302992
MA0067.1	0.924196
MA0068.1	0.111262
MA0069.1	0.607975
MA0070.1	0.597583
MA0071.1	0.27142
MA0072.1	0.593415
MA0073.1	0.000143211
MA0074.1	0.298586
MA0076.1	0.164578
MA0077.1	0.586275
MA0078.1	0.995054
MA0081.1	0.465308
MA0083.1	0.628701
MA0084.1	1.10674
MA0087.1	1.44255
MA0088.1	0.0797435
MA0089.1	0
MA0090.1	0.518617
MA0091.1	0.223914
MA0092.1	1.08245
MA0093.1	0.740148
MA0095.1	0
MA0098.1	0
MA0100.1	0.843378
MA0101.1	0.116395
MA0103.1	0.34743
MA0105.1	0.14145
MA0106.1	0.33677
MA0107.1	0.0748038
MA0108.2	1.18798
MA0109.1	0
MA0111.1	0.184188
MA0113.1	0.924932
MA0114.1	0.072201
MA0115.1	0.850405
MA0116.1	0.0765991
MA0117.1	0.656858
MA0119.1	0.142224
MA0122.1	0.681203
MA0124.1	0.810546
MA0125.1	0.730403
MA0130.1	0
MA0131.1	0.398042
MA0132.1	0
MA0133.1	0
MA0135.1	0.650071
MA0136.1	0.830767
MA0139.1	0.327572
MA0140.1	0.74193
MA0141.1	0.462123
MA0142.1	0.445733
MA0143.1	0.350722
MA0144.1	0.231909
MA0145.1	0.0322091
MA0146.1	0.603856
MA0147.1	0.269778
MA0148.1	0.240905
MA0149.1	0.261654
MA0062.2	0.148712
MA0035.2	0.268747
MA0039.2	0.750837
MA0138.2	0.38342
MA0002.2	0.393994
MA0137.2	0.398112
MA0104.2	0.420925
MA0047.2	0.326636
MA0112.2	0.339585
MA0065.2	0.033787
MA0150.1	0.98029
MA0151.1	0
MA0152.1	1.381
MA0153.1	0.714423
MA0154.1	0.137179
MA0155.1	0.025611
MA0156.1	0.12788
MA0157.1	0.421609
MA0158.1	0
MA0159.1	0.270712
MA0160.1	0.252705
MA0161.1	0
MA0162.1	0.259032
MA0163.1	0.00623
MA0164.1	0.361105
MA0080.2	0.740384
MA0018.2	0.337929
MA0099.2	0.754549
MA0079.2	0.00137008
MA0102.2	1.14323
MA0258.1	0.218609
MA0259.1	0.28219
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
BATF#10538	4	5.73124748054203	0.00439453342989944	0.020823987154504
BCL11A#53335	5	8.34395738341384	0.000235586408911819	0.00256723799669673
EBF1#1879	9	4.71518833053653	2.94711196653903e-05	0.000614235535169367
GATA3#2625	4	6.40859208404847	0.00294238410040412	0.0156993794350723
MEF2A#4205	5	5.51271497342472	0.00155536061245248	0.00987839376088085
MEF2C#4208	4	9.72031870414684	0.000633837963732913	0.00520174470330832
NFKB1#4790	13	4.19675438320705	2.76672721519416e-07	1.40405356476027e-05
POU2F2#5452	9	4.82088920704016	2.46150792069039e-05	0.000533577056307562
SMC3#9126	5	4.42498024850966	0.00407692658877639	0.0194780483076494
SPI1#6688	8	3.86085812165775	0.000424519206096243	0.00396781469173845
SRF#6722	6	4.86959232782393	0.000889959927249778	0.00662956667917543
USF2#7392	7	5.34972833502865	0.000155419582796084	0.00198070357628313

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.