Coexpression cluster:C1766

Full id: C1766_CD14_CD14CD16_Hair_CD8_CD19_xeroderma_CD4

Phase1 CAGE Peaks

Hg19::chr16:67970711..67970770,-	p1@PSMB10
Hg19::chr6:32806506..32806579,-	p1@TAP2
Hg19::chr6:32811771..32811831,-	p1@PSMB8
Hg19::chr6:32821924..32821931,+	p3@PSMB9
Hg19::chr6:32821956..32821975,+	p1@PSMB9

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
1.46259452862696e-08	9.05665559813991e-06	3	45	Proteasome (KEGG):03050
4.292253837981e-08	9.05665559813991e-06	3	64	Proteasome Degradation (Wikipathways):WP183
2.67613900622899e-07	4.23498997735737e-05	3	117	Cell Cycle Checkpoints (Reactome):REACT_1538
1.34823063570187e-06	9.48255547110314e-05	3	200	DNA Replication (Reactome):REACT_383
5.28055171391627e-06	0.0003342589234909	3	315	Cell Cycle, Mitotic (Reactome):REACT_152
7.41609277987709e-07	7.82397788277033e-05	3	164	Metabolism of RNA (Reactome):REACT_21257
4.292253837981e-08	9.05665559813991e-06	3	64	Signaling by Wnt (Reactome):REACT_11045
5.33165031389329e-07	6.7498692973889e-05	3	147	Apoptosis (Reactome):REACT_578
1.23011302483476e-06	9.48255547110314e-05	3	194	HIV Infection (Reactome):REACT_6185
1.24930054759413e-06	9.48255547110314e-05	3	195	Metabolism of amino acids and derivatives (Reactome):REACT_13
6.99828407380497e-06	0.000402719438065322	3	346	{CDC2,351} (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:0004298	threonine endopeptidase activity	4.45890006046998e-07
GO:0005839	proteasome core complex (sensu Eukaryota)	4.45890006046998e-07
GO:0000502	proteasome complex (sensu Eukaryota)	1.67734810946468e-06
GO:0005829	cytosol	2.45545651619859e-06
GO:0006955	immune response	3.17272568259787e-05
GO:0006511	ubiquitin-dependent protein catabolic process	3.17272568259787e-05
GO:0043632	modification-dependent macromolecule catabolic process	3.17272568259787e-05
GO:0019941	modification-dependent protein catabolic process	3.17272568259787e-05
GO:0051603	proteolysis involved in cellular protein catabolic process	3.17272568259787e-05
GO:0044257	cellular protein catabolic process	3.17272568259787e-05
GO:0002376	immune system process	3.18547758936163e-05
GO:0030163	protein catabolic process	4.79337041589452e-05
GO:0043285	biopolymer catabolic process	9.17363901730058e-05
GO:0044265	cellular macromolecule catabolic process	0.000130138439451392
GO:0009057	macromolecule catabolic process	0.000207011545222337
GO:0004175	endopeptidase activity	0.000372993694047045
GO:0043234	protein complex	0.000372993694047045
GO:0044248	cellular catabolic process	0.000372993694047045
GO:0009056	catabolic process	0.000612888261624961
GO:0004409	homoaconitate hydratase activity	0.000747674555516307
GO:0032991	macromolecular complex	0.00103080130692212
GO:0016787	hydrolase activity	0.00103483066727459
GO:0008233	peptidase activity	0.00103483066727459
GO:0006508	proteolysis	0.00119483757108028
GO:0046967	cytosol to ER transport	0.00119622646674452
GO:0044444	cytoplasmic part	0.00149521705842028
GO:0015440	peptide-transporting ATPase activity	0.00149521705842028
GO:0042825	TAP complex	0.00149521705842028
GO:0046980	tapasin binding	0.00149521705842028
GO:0015433	peptide antigen-transporting ATPase activity	0.00149521705842028
GO:0046978	TAP1 binding	0.00175900121882525
GO:0046977	TAP binding	0.00175900121882525
GO:0042824	MHC class I peptide loading complex	0.00175900121882525
GO:0046979	TAP2 binding	0.00175900121882525
GO:0042301	phosphate binding	0.00249169833156373
GO:0015198	oligopeptide transporter activity	0.00249169833156373
GO:0019538	protein metabolic process	0.00303212289754489
GO:0015197	peptide transporter activity	0.00314713046787477
GO:0042288	MHC class I protein binding	0.00344958683718131
GO:0002483	antigen processing and presentation of endogenous peptide antigen	0.00583164475744578
GO:0019885	antigen processing and presentation of endogenous peptide antigen via MHC class I	0.00583164475744578
GO:0006857	oligopeptide transport	0.00604832873003494
GO:0042605	peptide antigen binding	0.00611274679452986
GO:0019883	antigen processing and presentation of endogenous antigen	0.00611274679452986
GO:0005737	cytoplasm	0.00663599333603718
GO:0042287	MHC protein binding	0.00746948551180881
GO:0043231	intracellular membrane-bound organelle	0.011881802746805
GO:0043227	membrane-bound organelle	0.011881802746805
GO:0015833	peptide transport	0.011881802746805
GO:0005788	endoplasmic reticulum lumen	0.0190872887198677
GO:0006959	humoral immune response	0.0219186774220755
GO:0043229	intracellular organelle	0.0241778826458626
GO:0043226	organelle	0.0241778826458626
GO:0016836	hydro-lyase activity	0.0248247132780344
GO:0043170	macromolecule metabolic process	0.0264901850198828
GO:0016835	carbon-oxygen lyase activity	0.0264901850198828
GO:0002474	antigen processing and presentation of peptide antigen via MHC class I	0.0264901850198828
GO:0046982	protein heterodimerization activity	0.0264901850198828
GO:0048002	antigen processing and presentation of peptide antigen	0.0264901850198828
GO:0044267	cellular protein metabolic process	0.0329518394413252
GO:0044260	cellular macromolecule metabolic process	0.0336207880593579
GO:0042803	protein homodimerization activity	0.03784391734532
GO:0005634	nucleus	0.0395329301440715
GO:0044238	primary metabolic process	0.0395329301440715
GO:0003823	antigen binding	0.0404041470685052
GO:0044424	intracellular part	0.040719536022715
GO:0042277	peptide binding	0.0460001800729374

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	4.94e-51	136
nongranular leukocyte	2.76e-48	115
hematopoietic cell	3.46e-41	177
hematopoietic lineage restricted progenitor cell	4.07e-41	120
hematopoietic stem cell	8.96e-41	168
angioblastic mesenchymal cell	8.96e-41	168
hematopoietic oligopotent progenitor cell	1.81e-37	161
hematopoietic multipotent progenitor cell	1.81e-37	161
lymphocyte	2.51e-25	53
common lymphoid progenitor	2.51e-25	53
lymphoid lineage restricted progenitor cell	4.49e-25	52
nucleate cell	6.17e-23	55
myeloid leukocyte	6.28e-21	72
macrophage dendritic cell progenitor	6.86e-21	61
monopoietic cell	1.03e-20	59
monocyte	1.03e-20	59
monoblast	1.03e-20	59
promonocyte	1.03e-20	59
granulocyte monocyte progenitor cell	3.23e-18	67
defensive cell	1.58e-17	48
phagocyte	1.58e-17	48
myeloid lineage restricted progenitor cell	3.65e-16	66
connective tissue cell	5.59e-16	361
mesenchymal cell	6.46e-16	354
classical monocyte	6.50e-16	42
CD14-positive, CD16-negative classical monocyte	6.50e-16	42
myeloid cell	2.48e-14	108
common myeloid progenitor	2.48e-14	108
lymphocyte of B lineage	9.12e-13	24
pro-B cell	9.12e-13	24
multi fate stem cell	2.87e-12	427
T cell	3.35e-12	25
pro-T cell	3.35e-12	25
motile cell	8.44e-12	386
somatic stem cell	2.15e-11	433
stem cell	1.13e-10	441
mature alpha-beta T cell	4.04e-10	18
alpha-beta T cell	4.04e-10	18
immature T cell	4.04e-10	18
mature T cell	4.04e-10	18
immature alpha-beta T cell	4.04e-10	18
native cell	4.54e-09	722
B cell	1.15e-08	14
somatic cell	1.33e-08	588
CD8-positive, alpha-beta T cell	3.66e-07	11

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	4.87e-29	108
hematopoietic system	4.24e-27	98
blood island	4.24e-27	98
immune system	9.23e-22	93
bone marrow	2.14e-17	76
connective tissue	2.38e-15	371
bone element	8.44e-14	82
skeletal element	4.86e-12	90
lateral plate mesoderm	2.89e-11	203
skeletal system	2.29e-10	100
blood	1.01e-08	15
haemolymphatic fluid	1.01e-08	15
organism substance	1.01e-08	15

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	1.80249
MA0004.1	0.626788
MA0006.1	0.452993
MA0007.1	0.606704
MA0009.1	1.11255
MA0014.1	0.660087
MA0017.1	0.496101
MA0019.1	0.784036
MA0024.1	1.00439
MA0025.1	1.24931
MA0027.1	2.73598
MA0028.1	0.470679
MA0029.1	1.02437
MA0030.1	1.01252
MA0031.1	0.945567
MA0038.1	0.736268
MA0040.1	1.03042
MA0041.1	0.64667
MA0042.1	0.612397
MA0043.1	1.11288
MA0046.1	1.10134
MA0048.1	0.569896
MA0050.1	6.28581
MA0051.1	7.0616
MA0052.1	1.03442
MA0055.1	0.0853006
MA0056.1	0
MA0057.1	0.554727
MA0058.1	0.523638
MA0059.1	0.522232
MA0060.1	0.321781
MA0061.1	0.291022
MA0063.1	0
MA0066.1	0.736721
MA0067.1	1.43651
MA0068.1	0.692739
MA0069.1	1.09737
MA0070.1	1.08584
MA0071.1	0.695094
MA0072.1	1.0812
MA0073.1	0.0469445
MA0074.1	0.730989
MA0076.1	0.540943
MA0077.1	1.07324
MA0078.1	0.836493
MA0081.1	0.522409
MA0083.1	1.12028
MA0084.1	1.62584
MA0087.1	1.07867
MA0088.1	0.412364
MA0089.1	0
MA0090.1	0.556637
MA0091.1	0.629594
MA0092.1	0.588959
MA0093.1	0.456342
MA0095.1	0
MA0098.1	0
MA0100.1	0.750974
MA0101.1	0.459973
MA0103.1	0.442769
MA0105.1	0.520776
MA0106.1	0.779931
MA0107.1	0.378225
MA0108.2	0.94238
MA0109.1	0
MA0111.1	1.40074
MA0113.1	0.797251
MA0114.1	0.973423
MA0115.1	1.35895
MA0116.1	0.382106
MA0117.1	1.1512
MA0119.1	0.504689
MA0122.1	1.17777
MA0124.1	1.31673
MA0125.1	1.23103
MA0130.1	0
MA0131.1	0.855546
MA0132.1	0
MA0133.1	0
MA0135.1	1.14377
MA0136.1	0.743749
MA0139.1	2.96863
MA0140.1	0.692258
MA0141.1	1.29278
MA0142.1	0.912455
MA0143.1	0.797437
MA0144.1	0.356507
MA0145.1	0.143698
MA0146.1	0.6031
MA0147.1	0.386018
MA0148.1	0.653474
MA0149.1	0.681935
MA0062.2	0.284987
MA0035.2	0.691506
MA0039.2	0.527987
MA0138.2	0.837782
MA0002.2	0.30855
MA0137.2	0.47779
MA0104.2	0.320919
MA0047.2	0.767096
MA0112.2	0.136971
MA0065.2	0.880827
MA0150.1	1.35623
MA0151.1	0
MA0152.1	0.69926
MA0153.1	1.21379
MA0154.1	0.172764
MA0155.1	0.409315
MA0156.1	0.480289
MA0157.1	0.883854
MA0158.1	0
MA0159.1	1.00463
MA0160.1	0.669748
MA0161.1	0
MA0162.1	0.0592265
MA0163.1	0.0439995
MA0164.1	0.810347
MA0080.2	1.15604
MA0018.2	0.781393
MA0099.2	0.699641
MA0079.2	0.230892
MA0102.2	1.66336
MA0258.1	0.345771
MA0259.1	0.395396
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
ELF1#1997	5	4.25809795880754	0.000714241693977684	0.00573099940667912
GATA3#2625	2	10.8946065428824	0.012515829121883	0.0452830554167652
GTF2F1#2962	3	7.64379652605459	0.0042841549641205	0.0203461807238316
IRF1#3659	5	7.6371637535639	3.84754333311872e-05	0.000724154943535027
MEF2C#4208	2	16.5245417970496	0.00557985007798205	0.0252449299209135
NANOG#79923	2	11.6979113924051	0.0109116495195608	0.0402231315887834
NFKB1#4790	5	5.48806342419384	0.000200816284746232	0.00239036379788143
PAX5#5079	4	5.33565242494226	0.00222338958618779	0.0127783724957003
PRDM1#639	3	79.0985734664765	4.30606791165081e-06	0.000136196676748909
RAD21#5885	3	6.2130203372738	0.00775105506881164	0.031893169976031
REST#5978	3	5.79001722967681	0.00946878869443394	0.0356968856245889
RFX5#5993	4	9.63832866175608	0.00022148012581572	0.00249634824736326
SIN3A#25942	5	5.40888472681514	0.000215952267165727	0.00248035179044555
SMARCB1#6598	4	14.6021726249259	4.30486693344344e-05	0.000768408815009228
SMC3#9126	3	9.0269597069597	0.00265096444946755	0.014637276031612
STAT1#6772	4	16.5652699977594	2.61308619905866e-05	0.000563626826814306
STAT2#6773	4	52.2110169491525	2.71660181075469e-07	1.3976314113961e-05
STAT3#6774	3	6.31167899829254	0.00741117212246054	0.0306128541883268
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135322568524649
TBP#6908	5	3.70677068709639	0.00142875510672112	0.00918715395830854
YY1#7528	4	3.92893659988308	0.00719386626991762	0.0298403447201496
ZEB1#6935	3	10.1330592105263	0.00189555692435707	0.0111614179186406
ZNF143#7702	3	8.10052593133674	0.00362487051209098	0.0183304048521895

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.