Coexpression cluster:C411

Full id: C411_vagina_Mast_breast_heart_CD14_aorta_liver

Phase1 CAGE Peaks

Hg19::chr11:133904003..133904027,-	p@chr11:133904003..133904027 -
Hg19::chr11:133907166..133907180,+	p2@ENST00000531938
Hg19::chr11:133907234..133907249,+	p3@ENST00000531938
Hg19::chr11:133907376..133907387,+	p5@ENST00000531938
Hg19::chr11:65374430..65374474,-	p5@MAP3K11
Hg19::chr12:2903742..2903763,-	p3@CBX3P4
Hg19::chr12:2903775..2903794,-	p2@CBX3P4
Hg19::chr12:57082286..57082368,+	p@chr12:57082286..57082368 +
Hg19::chr13:31736027..31736053,-	p1@HSPH1
Hg19::chr14:70195360..70195363,-	p@chr14:70195360..70195363 -
Hg19::chr14:77924458..77924475,+	p2@AHSA1
Hg19::chr16:87378830..87378846,-	p@chr16:87378830..87378846 -
Hg19::chr16:89930250..89930272,-	p1@AK098674
Hg19::chr16:89930279..89930301,-	p2@AK098674
Hg19::chr18:19284854..19284899,+	p2@MIB1
Hg19::chr19:14629195..14629216,-	p1@DNAJB1
Hg19::chr1:245026181..245026208,-	p19@HNRNPU
Hg19::chr22:43041411..43041417,+	p@chr22:43041411..43041417 +
Hg19::chr4:88343933..88343946,+	p6@NUDT9
Hg19::chr6:31783311..31783328,+	p1@HSPA1A p1@HSPA1B
Hg19::chr6:31789738..31789757,-	p@chr6:31789738..31789757 -
Hg19::chr6:31795506..31795525,+	p2@HSPA1A p2@HSPA1B
Hg19::chr7:75923952..75923971,-	p@chr7:75923952..75923971 -
Hg19::chr7:75924283..75924306,+	p@chr7:75924283..75924306 +
Hg19::chr7:75931755..75931775,-	p@chr7:75931755..75931775 -

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
2.54761513593594e-05	0.0161264038104745	2	32	{HSPA8,34} (Static Module):NA

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:0051789	response to protein stimulus	5.16481965377491e-05
GO:0006986	response to unfolded protein	5.16481965377491e-05
GO:0009607	response to biotic stimulus	0.00408991908245404
GO:0006950	response to stress	0.0113033427993079
GO:0030189	chaperone activator activity	0.0131932179441893
GO:0042221	response to chemical stimulus	0.0167213722932249
GO:0019144	ADP-sugar diphosphatase activity	0.0183373558696005
GO:0005737	cytoplasm	0.0183373558696005
GO:0047631	ADP-ribose diphosphatase activity	0.0197851668314843
GO:0004706	JUN kinase kinase kinase activity	0.0197851668314843
GO:0051082	unfolded protein binding	0.0273491196999661
GO:0001671	ATPase activator activity	0.0274729278152382
GO:0005739	mitochondrion	0.0320692916310955
GO:0001947	heart looping	0.0320692916310955
GO:0044424	intracellular part	0.0320692916310955
GO:0045665	negative regulation of neuron differentiation	0.0320692916310955
GO:0051085	chaperone cofactor-dependent protein folding	0.0320692916310955
GO:0016071	mRNA metabolic process	0.0320692916310955
GO:0044444	cytoplasmic part	0.0320692916310955
GO:0006457	protein folding	0.0320692916310955
GO:0005524	ATP binding	0.0320692916310955
GO:0032559	adenyl ribonucleotide binding	0.0320692916310955
GO:0003007	heart morphogenesis	0.0320692916310955
GO:0051084	'de novo' posttranslational protein folding	0.0320692916310955
GO:0001839	neural plate morphogenesis	0.0320692916310955
GO:0051087	chaperone binding	0.0320692916310955
GO:0001841	neural tube formation	0.0320692916310955
GO:0006458	'de novo' protein folding	0.0320692916310955
GO:0001840	neural plate development	0.0320692916310955
GO:0000080	G1 phase of mitotic cell cycle	0.0320692916310955
GO:0001838	embryonic epithelial tube formation	0.0320692916310955
GO:0045807	positive regulation of endocytosis	0.0320692916310955
GO:0030530	heterogeneous nuclear ribonucleoprotein complex	0.0320692916310955
GO:0004709	MAP kinase kinase kinase activity	0.0320692916310955
GO:0001756	somitogenesis	0.0320692916310955
GO:0030554	adenyl nucleotide binding	0.0320692916310955
GO:0046328	regulation of JNK cascade	0.0320692916310955
GO:0051318	G1 phase	0.0320692916310955
GO:0021915	neural tube development	0.0320692916310955
GO:0007257	activation of JNK activity	0.0343930784770196
GO:0016331	morphogenesis of embryonic epithelium	0.0343930784770196
GO:0043229	intracellular organelle	0.0343930784770196
GO:0043226	organelle	0.0343930784770196
GO:0043507	positive regulation of JNK activity	0.0343930784770196
GO:0043506	regulation of JNK activity	0.0365444265241635
GO:0045664	regulation of neuron differentiation	0.0371756059842438
GO:0035282	segmentation	0.037779597917854
GO:0006402	mRNA catabolic process	0.0397233584196399
GO:0005227	calcium activated cation channel activity	0.0446830244551175
GO:0030100	regulation of endocytosis	0.0446830244551175
GO:0032553	ribonucleotide binding	0.0447701239990005
GO:0032555	purine ribonucleotide binding	0.0447701239990005
GO:0051050	positive regulation of transport	0.047090896044346
GO:0017076	purine nucleotide binding	0.0491008753794253

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
classical monocyte	7.51e-07	42
CD14-positive, CD16-negative classical monocyte	7.51e-07	42

Uber Anatomy

Ontology term	p-value	n
adult organism	1.99e-41	114
neural tube	2.64e-26	56
neural rod	2.64e-26	56
future spinal cord	2.64e-26	56
neural keel	2.64e-26	56
regional part of nervous system	7.07e-24	53
regional part of brain	7.07e-24	53
neurectoderm	3.22e-20	86
neural plate	5.62e-20	82
presumptive neural plate	5.62e-20	82
brain	1.05e-16	68
future brain	1.05e-16	68
regional part of forebrain	1.49e-16	41
forebrain	1.49e-16	41
anterior neural tube	1.49e-16	41
future forebrain	1.49e-16	41
central nervous system	1.53e-15	81
nervous system	2.03e-14	89
brainstem	4.30e-14	6
ecto-epithelium	5.60e-14	104
brain grey matter	7.78e-13	34
gray matter	7.78e-13	34
telencephalon	1.09e-12	34
posterior neural tube	2.17e-11	15
chordal neural plate	2.17e-11	15
structure with developmental contribution from neural crest	5.12e-11	132
pre-chordal neural plate	1.14e-10	61
regional part of telencephalon	2.53e-10	32
cerebral hemisphere	4.45e-10	32
neural nucleus	5.51e-09	9
nucleus of brain	5.51e-09	9
segmental subdivision of hindbrain	6.56e-09	12
hindbrain	6.56e-09	12
presumptive hindbrain	6.56e-09	12
medulla oblongata	2.15e-08	3
myelencephalon	2.15e-08	3
future myelencephalon	2.15e-08	3
segmental subdivision of nervous system	3.89e-08	13
regional part of cerebral cortex	6.99e-08	22
organ system subdivision	9.09e-08	223
pons	2.18e-07	3
organ	3.45e-07	503
ectoderm-derived structure	3.71e-07	171
ectoderm	3.71e-07	171
presumptive ectoderm	3.71e-07	171
neocortex	5.08e-07	20
tube	7.55e-07	192
cerebral cortex	9.50e-07	25
pallium	9.50e-07	25

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	1.32414
MA0004.1	0.812914
MA0006.1	0.194765
MA0007.1	0.120068
MA0009.1	0.480543
MA0014.1	2.54242
MA0017.1	0.242343
MA0019.1	0.227177
MA0024.1	0.391254
MA0025.1	0.599238
MA0027.1	2.03861
MA0028.1	1.23143
MA0029.1	0.407394
MA0030.1	0.397801
MA0031.1	0.344829
MA0038.1	1.7022
MA0040.1	0.412311
MA0041.1	0.141769
MA0042.1	0.123063
MA0043.1	0.480818
MA0046.1	0.47108
MA0048.1	0.128228
MA0050.1	0.390696
MA0051.1	0.562815
MA0052.1	0.41557
MA0055.1	0.601885
MA0056.1	0
MA0057.1	1.0874
MA0058.1	0.274844
MA0059.1	0.273146
MA0060.1	1.7471
MA0061.1	1.52142
MA0063.1	0
MA0066.1	0.570377
MA0067.1	0.769322
MA0068.1	2.41944
MA0069.1	0.467738
MA0070.1	0.458064
MA0071.1	0.170069
MA0072.1	0.454189
MA0073.1	3.45441
MA0074.1	0.561594
MA0076.1	1.03285
MA0077.1	1.1369
MA0078.1	0.263604
MA0081.1	0.27336
MA0083.1	0.487092
MA0084.1	0.947429
MA0087.1	0.452083
MA0088.1	3.66743
MA0089.1	0
MA0090.1	0.0951695
MA0091.1	0.132307
MA0092.1	0.357807
MA0093.1	0.766566
MA0095.1	0
MA0098.1	0
MA0100.1	0.592379
MA0101.1	1.18678
MA0103.1	0.049017
MA0105.1	2.34733
MA0106.1	1.19314
MA0107.1	0.539977
MA0108.2	1.62457
MA0109.1	0
MA0111.1	0.102187
MA0113.1	0.665323
MA0114.1	0.118114
MA0115.1	0.697973
MA0116.1	0.550701
MA0117.1	0.513502
MA0119.1	0.916487
MA0122.1	0.53644
MA0124.1	0.659634
MA0125.1	0.583056
MA0130.1	0
MA0131.1	2.1352
MA0132.1	0
MA0133.1	0
MA0135.1	0.507125
MA0136.1	0.581198
MA0139.1	0.748833
MA0140.1	0.168354
MA0141.1	0.270862
MA0142.1	0.319458
MA0143.1	0.236302
MA0144.1	3.65785
MA0145.1	2.24107
MA0146.1	1.46595
MA0147.1	0.306717
MA0148.1	0.145617
MA0149.1	0.94608
MA0062.2	0.78545
MA0035.2	0.167901
MA0039.2	7.97659
MA0138.2	0.264522
MA0002.2	0.359117
MA0137.2	3.5878
MA0104.2	0.200815
MA0047.2	0.215827
MA0112.2	0.10763
MA0065.2	0.535761
MA0150.1	0.307678
MA0151.1	0
MA0152.1	0.172601
MA0153.1	0.567879
MA0154.1	0.488003
MA0155.1	0.625371
MA0156.1	0.487034
MA0157.1	0.298026
MA0158.1	0
MA0159.1	0.563553
MA0160.1	0.154993
MA0161.1	0
MA0162.1	2.01892
MA0163.1	0.870896
MA0164.1	0.245213
MA0080.2	0.438824
MA0018.2	0.640077
MA0099.2	0.172833
MA0079.2	10.7306
MA0102.2	0.983247
MA0258.1	0.0222068
MA0259.1	1.78654
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
BRCA1#672	5	4.03684612864475	0.00689254689097077	0.0291874753576652
CCNT2#905	14	3.54827288309908	4.62126213135399e-06	0.00014368561945117
EBF1#1879	10	3.5625867386276	0.000209250484315379	0.00243687682107648
EGR1#1958	13	2.59385312930127	0.00037778572640151	0.00374661128854309
EP300#2033	9	2.43861902144035	0.00717124881905474	0.0297784603162204
GATA3#2625	6	6.53676392572944	0.000236828365665375	0.00257942618434937
GTF2B#2959	6	7.66651918423782	9.94934489292016e-05	0.00140040381573004
GTF2F1#2962	7	3.56710504549214	0.00248487859809469	0.0139555945314267
HMGN3#9324	12	3.92570290720828	1.23148160281096e-05	0.000304197509735037
HSF1#3297	11	72.2878933333333	1.66913017282451e-18	3.78961491564389e-16
IRF1#3659	12	3.66583860171067	2.49394930213504e-05	0.000539936921985244
MXI1#4601	9	3.58616578635335	0.000470323889250828	0.00431825553138173
NFKB1#4790	12	2.63427044361304	0.000648461623178439	0.00531340683062396
POLR2A#5430	21	1.80386066830878	0.000129903105445809	0.00171062292644747
PPARGC1A#10891	8	112.016363636364	4.35959567622917e-15	7.71714936999488e-13
PRDM1#639	3	15.8197146932953	0.000884249246251442	0.0065926689769599
RDBP#7936	4	24.582144638404	2.02574085028561e-05	0.000449471741370254
SIN3A#25942	10	2.16355389072605	0.0100430877544989	0.0376540078256789
SRF#6722	6	3.31132278292027	0.0077135267669906	0.0317512621006515
STAT1#6772	5	4.14131749943984	0.00619545137151441	0.027376634050755
STAT2#6773	4	10.4422033898305	0.000537967092450348	0.00464797693319176
STAT3#6774	10	4.2077859988617	5.1112914742446e-05	0.000870403016922602
TAF1#6872	16	2.13954962287699	0.000436887104077226	0.00407247878103547
TAF7#6879	8	3.65858220957565	0.00094706251346002	0.00685258846080443
TBP#6908	13	1.92752075729012	0.00683471173406966	0.0289825189327419
TCF12#6938	7	2.9776501726122	0.00680129072796867	0.0288419685860939
TFAP2C#7022	8	3.45895315515527	0.00136807008625109	0.0090014409209335
ZBTB33#10009	4	5.06635600479698	0.00739199014156867	0.0305457014479422

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.