Coexpression cluster:C3732

Full id: C3732_migratory_immature_CD14_Astrocyte_papillotubular_clear_mycosis

Phase1 CAGE Peaks

Hg19::chr18:56338688..56338708,+	p1@MALT1
Hg19::chr1:995067..995099,+	p1@uc009vjs.1
Hg19::chr1:995102..995125,+	p1@ENST00000427998 p1@uc001acl.1

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:0032449	CBM complex	0.00240315553985635
GO:0002711	positive regulation of T cell mediated immunity	0.00240315553985635
GO:0032743	positive regulation of interleukin-2 production	0.00240315553985635
GO:0002726	positive regulation of T cell cytokine production	0.00240315553985635
GO:0002369	T cell cytokine production	0.00240315553985635
GO:0002724	regulation of T cell cytokine production	0.00240315553985635
GO:0002702	positive regulation of production of molecular mediator of immune response	0.00240315553985635
GO:0002720	positive regulation of cytokine production during immune response	0.00240315553985635
GO:0002709	regulation of T cell mediated immunity	0.00240315553985635
GO:0032663	regulation of interleukin-2 production	0.00240315553985635
GO:0002824	positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.00240315553985635
GO:0002718	regulation of cytokine production during immune response	0.00240315553985635
GO:0002821	positive regulation of adaptive immune response	0.00240315553985635
GO:0002700	regulation of production of molecular mediator of immune response	0.00240315553985635
GO:0002367	cytokine production during immune response	0.00240315553985635
GO:0043621	protein self-association	0.00240315553985635
GO:0002705	positive regulation of leukocyte mediated immunity	0.00240315553985635
GO:0002456	T cell mediated immunity	0.00240315553985635
GO:0002708	positive regulation of lymphocyte mediated immunity	0.00240315553985635
GO:0002699	positive regulation of immune effector process	0.00240315553985635
GO:0007250	activation of NF-kappaB-inducing kinase	0.00240315553985635
GO:0002703	regulation of leukocyte mediated immunity	0.00240315553985635
GO:0002706	regulation of lymphocyte mediated immunity	0.00240315553985635
GO:0002819	regulation of adaptive immune response	0.00240315553985635
GO:0002822	regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains.	0.00240315553985635
GO:0002697	regulation of immune effector process	0.00266622286226666
GO:0050852	T cell receptor signaling pathway	0.00290980371635028
GO:0019209	kinase activator activity	0.00297093404652571
GO:0032623	interleukin-2 production	0.0033465693857416
GO:0001819	positive regulation of cytokine production	0.0035431139369677
GO:0002440	production of molecular mediator of immune response	0.00389935093606499
GO:0050851	antigen receptor-mediated signaling pathway	0.00389935093606499
GO:0002429	immune response-activating cell surface receptor signaling pathway	0.00420132087387474
GO:0002768	immune response-regulating cell surface receptor signaling pathway	0.00421367769997437
GO:0002757	immune response-activating signal transduction	0.00422532842172546
GO:0002764	immune response-regulating signal transduction	0.00423633188115703
GO:0050870	positive regulation of T cell activation	0.00498630451083555
GO:0001817	regulation of cytokine production	0.00498630451083555
GO:0051168	nuclear export	0.00521394693065481
GO:0030693	caspase activity	0.00574863661035056
GO:0051251	positive regulation of lymphocyte activation	0.00574863661035056
GO:0050863	regulation of T cell activation	0.00649204106463026
GO:0051259	protein oligomerization	0.00666349031623854
GO:0032147	activation of protein kinase activity	0.00716796785828425
GO:0002253	activation of immune response	0.00716796785828425
GO:0002449	lymphocyte mediated immunity	0.00716796785828425
GO:0002250	adaptive immune response	0.00716796785828425
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.00716796785828425
GO:0051249	regulation of lymphocyte activation	0.00716796785828425
GO:0002443	leukocyte mediated immunity	0.00720946661956905
GO:0050865	regulation of cell activation	0.00724933797845053
GO:0050778	positive regulation of immune response	0.00749896140884057
GO:0002684	positive regulation of immune system process	0.00749896140884057
GO:0050776	regulation of immune response	0.00810781221274073
GO:0042110	T cell activation	0.00810781221274073
GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB cascade	0.00810781221274073
GO:0002682	regulation of immune system process	0.00810781221274073
GO:0051240	positive regulation of multicellular organismal process	0.00836642346435401
GO:0043122	regulation of I-kappaB kinase/NF-kappaB cascade	0.00845960881044609
GO:0002252	immune effector process	0.00847266376231406
GO:0001816	cytokine production	0.00856105220692837
GO:0019207	kinase regulator activity	0.00909382679474178
GO:0007249	I-kappaB kinase/NF-kappaB cascade	0.0100831700972994
GO:0045860	positive regulation of protein kinase activity	0.0100831700972994
GO:0004197	cysteine-type endopeptidase activity	0.0100831700972994
GO:0033674	positive regulation of kinase activity	0.0100831700972994
GO:0051347	positive regulation of transferase activity	0.010139605750829
GO:0009967	positive regulation of signal transduction	0.0101541783374212
GO:0006913	nucleocytoplasmic transport	0.0101541783374212
GO:0046649	lymphocyte activation	0.0101541783374212
GO:0051169	nuclear transport	0.0101541783374212
GO:0004842	ubiquitin-protein ligase activity	0.0105090574187607
GO:0008639	small protein conjugating enzyme activity	0.0105090574187607
GO:0006916	anti-apoptosis	0.0106168513974943
GO:0045321	leukocyte activation	0.0110914871070293
GO:0001775	cell activation	0.0127089956434711
GO:0043066	negative regulation of apoptosis	0.0136242834052795
GO:0043069	negative regulation of programmed cell death	0.0136273612960296
GO:0045859	regulation of protein kinase activity	0.0138073039089563
GO:0019787	small conjugating protein ligase activity	0.0138073039089563
GO:0043549	regulation of kinase activity	0.0138073039089563
GO:0051338	regulation of transferase activity	0.0139207180662411
GO:0043085	positive regulation of catalytic activity	0.0142541199769051
GO:0051239	regulation of multicellular organismal process	0.0152397913127337
GO:0008234	cysteine-type peptidase activity	0.0160676097141558
GO:0016881	acid-amino acid ligase activity	0.0160676097141558
GO:0006461	protein complex assembly	0.0180608506532087
GO:0016879	ligase activity, forming carbon-nitrogen bonds	0.0194836255525941
GO:0007243	protein kinase cascade	0.0195243406003887
GO:0008047	enzyme activator activity	0.0233640121930479
GO:0006512	ubiquitin cycle	0.0278810733597028
GO:0042981	regulation of apoptosis	0.0286231925342692
GO:0043067	regulation of programmed cell death	0.0286231925342692
GO:0006952	defense response	0.0287120056316716
GO:0050790	regulation of catalytic activity	0.0294313583322489
GO:0016874	ligase activity	0.0311466673535068
GO:0065009	regulation of a molecular function	0.0319690199691438
GO:0065003	macromolecular complex assembly	0.0356512085583085
GO:0009966	regulation of signal transduction	0.0371102672789356
GO:0004175	endopeptidase activity	0.0371102672789356
GO:0022607	cellular component assembly	0.0372004084901602
GO:0006915	apoptosis	0.038676625753476
GO:0012501	programmed cell death	0.038676625753476
GO:0008219	cell death	0.0396747376863077
GO:0016265	death	0.0396747376863077
GO:0046907	intracellular transport	0.0396747376863077
GO:0048522	positive regulation of cellular process	0.0412043563088239
GO:0048518	positive regulation of biological process	0.0454442874524118
GO:0051649	establishment of cellular localization	0.0465537188207882
GO:0051641	cellular localization	0.0473068730398296
GO:0048523	negative regulation of cellular process	0.0473386668194157
GO:0048519	negative regulation of biological process	0.0486275006277944
GO:0006955	immune response	0.0486275006277944
GO:0008233	peptidase activity	0.0499116919816319
GO:0048468	cell development	0.0499116919816319

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
classical monocyte	2.14e-17	42
CD14-positive, CD16-negative classical monocyte	2.14e-17	42
defensive cell	4.58e-17	48
phagocyte	4.58e-17	48
granulocyte monocyte progenitor cell	3.52e-16	67
macrophage dendritic cell progenitor	1.49e-14	61
monopoietic cell	1.89e-13	59
monocyte	1.89e-13	59
monoblast	1.89e-13	59
promonocyte	1.89e-13	59
myeloid lineage restricted progenitor cell	2.62e-13	66
myeloid leukocyte	7.07e-13	72
epithelial cell	1.75e-10	253
leukocyte	1.35e-09	136
hematopoietic lineage restricted progenitor cell	3.52e-09	120
myeloid cell	1.73e-08	108
common myeloid progenitor	1.73e-08	108
kidney cell	2.39e-08	17
kidney epithelial cell	2.39e-08	17
nongranular leukocyte	4.76e-08	115
epithelial cell of nephron	2.20e-07	15
kidney tubule cell	5.73e-07	10
nephron tubule epithelial cell	5.73e-07	10

Uber Anatomy

Ontology term	p-value	n
skeletal element	3.33e-12	90
bone element	4.09e-12	82
bone marrow	2.12e-11	76
skeletal system	8.37e-10	100
immune system	1.73e-09	93
hematopoietic system	1.12e-08	98
blood island	1.12e-08	98
hemolymphoid system	1.21e-07	108
nephron epithelium	2.20e-07	15
renal tubule	2.20e-07	15
nephron tubule	2.20e-07	15
nephron	2.20e-07	15
uriniferous tubule	2.20e-07	15
nephrogenic mesenchyme	2.20e-07	15
organ	4.46e-07	503
excretory tube	4.79e-07	16
kidney epithelium	4.79e-07	16
nephron tubule epithelium	5.73e-07	10

Disease

Ontology term	p-value	n
carcinoma	1.15e-11	106
cell type cancer	1.08e-10	143
cancer	2.93e-08	235
disease of cellular proliferation	3.39e-08	239

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	6.06693
MA0004.1	0.826076
MA0006.1	0.639288
MA0007.1	0.804807
MA0009.1	1.3275
MA0014.1	4.7105
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	0.341392
MA0050.1	0.81185
MA0051.1	0.936307
MA0052.1	1.24796
MA0055.1	0.190716
MA0056.1	0
MA0057.1	0.333427
MA0058.1	0.716037
MA0059.1	0.714521
MA0060.1	0.492218
MA0061.1	0.456531
MA0063.1	0
MA0066.1	0.941452
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	0.0834661
MA0074.1	0.935474
MA0076.1	0.734647
MA0077.1	1.28751
MA0078.1	1.04495
MA0081.1	0.714712
MA0083.1	1.33535
MA0084.1	1.84562
MA0087.1	1.29304
MA0088.1	2.03569
MA0089.1	0
MA0090.1	0.751469
MA0091.1	0.829044
MA0092.1	0.785956
MA0093.1	0.642957
MA0095.1	0
MA0098.1	0
MA0100.1	0.956299
MA0101.1	0.646932
MA0103.1	0.628063
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	2.4174
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	3.00132
MA0147.1	0.565108
MA0148.1	0.854239
MA0149.1	0.884158
MA0062.2	1.141
MA0035.2	0.894194
MA0039.2	8.82315
MA0138.2	1.04628
MA0002.2	0.476938
MA0137.2	0.666381
MA0104.2	0.491226
MA0047.2	0.973066
MA0112.2	2.07067
MA0065.2	0.277623
MA0150.1	0.744617
MA0151.1	0
MA0152.1	0.902317
MA0153.1	1.43021
MA0154.1	0.312019
MA0155.1	1.31345
MA0156.1	0.669101
MA0157.1	1.09377
MA0158.1	0
MA0159.1	0.565904
MA0160.1	0.871361
MA0161.1	0
MA0162.1	2.05956
MA0163.1	1.2663
MA0164.1	1.01792
MA0080.2	0.643061
MA0018.2	0.987913
MA0099.2	0.902716
MA0079.2	2.28794
MA0102.2	1.88331
MA0258.1	1.29138
MA0259.1	2.40872
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
CTCFL#140690	2	13.1643162393162	0.00743336703699601	0.0306790523602777
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322020510383587
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462057356006245
TFAP2A#7020	2	11.0124229153633	0.0105499065521556	0.0390122044542217
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00615741060191452
THAP1#55145	2	20.9127630685675	0.00298344741373694	0.0158665986578711
ZEB1#6935	2	11.2589546783626	0.0101022267664633	0.0378132915655745

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.