Coexpression cluster:C2194

Full id: C2194_Mast_CD4_cord_embryonic_hepatoblastoma_cerebellum_lung

Phase1 CAGE Peaks

Hg19::chr12:123011476..123011527,-	p1@RSRC2
Hg19::chr12:123011536..123011547,-	p2@RSRC2
Hg19::chr21:30396966..30397025,+	p1@USP16
Hg19::chr3:14693247..14693293,+	p1@C3orf19

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:0004221	ubiquitin thiolesterase activity	0.0344053391563105
GO:0004843	ubiquitin-specific protease activity	0.0344053391563105
GO:0019783	small conjugating protein-specific protease activity	0.0344053391563105
GO:0004197	cysteine-type endopeptidase activity	0.0344053391563105
GO:0016790	thiolester hydrolase activity	0.0344053391563105
GO:0006511	ubiquitin-dependent protein catabolic process	0.0344053391563105
GO:0043632	modification-dependent macromolecule catabolic process	0.0344053391563105
GO:0019941	modification-dependent protein catabolic process	0.0344053391563105
GO:0051603	proteolysis involved in cellular protein catabolic process	0.0344053391563105
GO:0044257	cellular protein catabolic process	0.0344053391563105
GO:0008234	cysteine-type peptidase activity	0.0344053391563105
GO:0030163	protein catabolic process	0.0375505318105106
GO:0043285	biopolymer catabolic process	0.0442038239636262
GO:0044265	cellular macromolecule catabolic process	0.0463263864358884
GO:0006512	ubiquitin cycle	0.0463263864358884
GO:0009057	macromolecule catabolic process	0.0494432915342046

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
hematopoietic stem cell	7.52e-36	168
angioblastic mesenchymal cell	7.52e-36	168
leukocyte	1.02e-33	136
hematopoietic oligopotent progenitor cell	3.21e-33	161
hematopoietic multipotent progenitor cell	3.21e-33	161
hematopoietic cell	3.40e-33	177
hematopoietic lineage restricted progenitor cell	7.10e-27	120
nongranular leukocyte	1.16e-24	115
myeloid cell	1.29e-19	108
common myeloid progenitor	1.29e-19	108
classical monocyte	8.49e-18	42
CD14-positive, CD16-negative classical monocyte	8.49e-18	42
myeloid leukocyte	3.31e-16	72
granulocyte monocyte progenitor cell	6.12e-14	67
defensive cell	8.64e-14	48
phagocyte	8.64e-14	48
myeloid lineage restricted progenitor cell	1.41e-13	66
nucleate cell	1.83e-13	55
lymphocyte	9.82e-13	53
common lymphoid progenitor	9.82e-13	53
lymphoid lineage restricted progenitor cell	1.59e-12	52
macrophage dendritic cell progenitor	1.10e-11	61
monopoietic cell	7.01e-11	59
monocyte	7.01e-11	59
monoblast	7.01e-11	59
promonocyte	7.01e-11	59
mature alpha-beta T cell	1.83e-07	18
alpha-beta T cell	1.83e-07	18
immature T cell	1.83e-07	18
mature T cell	1.83e-07	18
immature alpha-beta T cell	1.83e-07	18

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	7.20e-15	98
blood island	7.20e-15	98
adult organism	8.46e-13	114
hemolymphoid system	3.54e-11	108
bone element	1.18e-10	82
bone marrow	1.21e-10	76
skeletal element	4.81e-09	90
immune system	2.08e-08	93
neural tube	2.45e-08	56
neural rod	2.45e-08	56
future spinal cord	2.45e-08	56
neural keel	2.45e-08	56
regional part of forebrain	3.82e-08	41
forebrain	3.82e-08	41
anterior neural tube	3.82e-08	41
future forebrain	3.82e-08	41
skeletal system	6.28e-08	100
regional part of nervous system	7.19e-08	53
regional part of brain	7.19e-08	53
nervous system	3.16e-07	89

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
ATF3#467	2	11.2315872630044	0.0111955903992222	0.0411217649892511
BCLAF1#9774	2	10.8263238050609	0.0120220381643258	0.0436461794362993
BRCA1#672	3	15.1381729824178	0.000468218442143119	0.00430005855425477
CEBPB#1051	3	5.97836071936861	0.00715383248472697	0.0297179551677499
CHD2#1106	4	10.3440228341169	8.73193255208051e-05	0.00128916356206776
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160609712086473
ELK4#2005	4	16.235681658468	1.43847748454449e-05	0.000342919767195485
EP300#2033	3	5.0804562946674	0.0114429840539824	0.0418743451861901
ESRRA#2101	1	120.960078534031	0.00824166246177904	0.032479943618948
ETS1#2113	3	7.29657069165175	0.0040085737751139	0.0191997907130989
FOS#2353	3	6.7484664816708	0.00503245277631794	0.0234552095459599
FOXA1#3169	3	8.31106481203909	0.00274013818210985	0.0150342680116296
GABPB1#2553	4	7.06768383618217	0.000400687686442317	0.00389822275587789
GTF2B#2959	3	23.9578724507432	0.000119775456285592	0.00162394247423224
GTF2F1#2962	4	12.7396608767577	3.79492332235515e-05	0.000716705238451085
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185641948352169
IRF1#3659	3	5.72787281517293	0.00809711479033333	0.0319960110324488
IRF4#3662	2	10.9572563433721	0.0117453018068803	0.0428230956679621
JUND#3727	3	5.24599795640327	0.0104343275174842	0.0386724415912039
MAX#4149	3	4.83941663175534	0.0131573713783684	0.0465984844988102
MXI1#4601	3	7.47117872156947	0.00374131473855096	0.0186270281727379
MYC#4609	4	5.2222818716094	0.00134430939527274	0.00886073391813754
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.00766804026811966
NFYA#4800	3	13.8191855248729	0.000613241180673451	0.00508465351447718
NFYB#4801	3	12.5698449401523	0.00081145639769735	0.00618460882428034
NR2C2#7182	2	16.3073054526204	0.00541182534464822	0.0245528074356957
NR3C1#2908	3	11.2297674983798	0.00113167206806385	0.00775275166392396
NRF1#4899	4	12.2102794477109	4.49717228915276e-05	0.000792307990396129
POU2F2#5452	4	9.10612405774252	0.00014539566517493	0.00188142459115407
PPARGC1A#10891	1	87.5127840909091	0.0113781217638372	0.0417042064607776
REST#5978	3	7.23752153709602	0.00410469730419261	0.0195722267156358
RFX5#5993	3	9.03593312039632	0.00214456119132407	0.0123825644770397
RXRA#6256	3	15.05596285435	0.000475830799730358	0.00433679142098254
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00794754450557103
SMARCB1#6598	3	13.6895368358681	0.000630578340937934	0.00517987819326859
SP2#6668	2	13.0767652469223	0.00833003653661494	0.0328034646449051
SPI1#6688	3	6.15324263139204	0.00658038711305903	0.0280911117801256
STAT1#6772	2	10.3532937485996	0.0131077747617126	0.0464874656458334
STAT2#6773	2	32.6318855932203	0.00137958877512552	0.0089827226985869
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.032139290269287
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0243591863043096
USF2#7392	3	9.7441480388022	0.00171834184841007	0.0107154229941545
XRCC4#7518	1	1074.57558139535	0.000930282808003446	0.00674332358308384
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106655513337327
ZNF143#7702	4	13.5008765522279	3.00867915035614e-05	0.000619892368877579
ZNF263#10127	3	6.16638122775801	0.00653981434797598	0.027961340757697

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.