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	4.65e-50	140
nongranular leukocyte	2.40e-46	119
hematopoietic cell	2.80e-41	182
hematopoietic stem cell	2.14e-40	172
angioblastic mesenchymal cell	2.14e-40	172
hematopoietic lineage restricted progenitor cell	2.89e-40	124
hematopoietic oligopotent progenitor cell	2.38e-37	165
hematopoietic multipotent progenitor cell	2.38e-37	165
lymphocyte	8.26e-25	53
common lymphoid progenitor	8.26e-25	53
lymphoid lineage restricted progenitor cell	1.45e-24	52
myeloid leukocyte	1.21e-20	76
macrophage dendritic cell progenitor	6.89e-20	65
monopoietic cell	1.42e-19	63
monocyte	1.42e-19	63
monoblast	1.42e-19	63
promonocyte	1.42e-19	63
granulocyte monocyte progenitor cell	6.63e-18	71
connective tissue cell	1.06e-16	365
CD14-positive, CD16-negative classical monocyte	1.15e-16	42
mesenchymal cell	1.41e-16	358
myeloid lineage restricted progenitor cell	7.96e-16	70
classical monocyte	4.50e-15	45
myeloid cell	1.32e-14	112
common myeloid progenitor	1.32e-14	112
multi fate stem cell	2.43e-13	430
lymphocyte of B lineage	6.99e-13	24
pro-B cell	6.99e-13	24
motile cell	2.13e-12	390
somatic stem cell	2.21e-12	436
T cell	7.08e-12	25
pro-T cell	7.08e-12	25
stem cell	1.52e-11	444
mature alpha-beta T cell	8.28e-10	18
alpha-beta T cell	8.28e-10	18
immature T cell	8.28e-10	18
mature T cell	8.28e-10	18
immature alpha-beta T cell	8.28e-10	18
native cell	1.79e-09	722
somatic cell	9.82e-09	591
B cell	1.53e-08	14
CD8-positive, alpha-beta T cell	4.64e-07	11

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	4.11e-29	112
hematopoietic system	5.65e-27	102
blood island	5.65e-27	102
immune system	3.90e-19	115
bone marrow	3.30e-17	80
connective tissue	3.66e-16	375
bone element	8.45e-14	86
lateral plate mesoderm	7.31e-12	216
skeletal element	5.68e-11	101
skeletal system	5.68e-11	101
blood	8.50e-09	15
haemolymphatic fluid	8.50e-09	15
organism substance	8.50e-09	15
musculoskeletal system	3.69e-07	167

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
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.