Coexpression cluster:C2145

Full id: C2145_Mesenchymal_Alveolar_Renal_Placental_nonsmall_Bronchial_left

Phase1 CAGE Peaks

Hg19::chr11:62439136..62439162,+	p1@C11orf83
Hg19::chr17:73900954..73901003,-	p1@MRPL38
Hg19::chr17:79670440..79670524,+	p1@MRPL12 p1@SLC25A10
Hg19::chr8:145149957..145150006,+	p1@CYC1

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:0005739	mitochondrion	0.00246685015740525
GO:0045155	electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity	0.0085656256290494
GO:0006390	transcription from mitochondrial promoter	0.0142747820013017
GO:0044429	mitochondrial part	0.0214058702371865
GO:0000315	organellar large ribosomal subunit	0.0214058702371865
GO:0005762	mitochondrial large ribosomal subunit	0.0214058702371865
GO:0005840	ribosome	0.0255028847072952
GO:0044444	cytoplasmic part	0.0299280631346191
GO:0030529	ribonucleoprotein complex	0.0354431211698454
GO:0000313	organellar ribosome	0.0396560987964519
GO:0005761	mitochondrial ribosome	0.0396560987964519

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
epithelial cell	3.44e-30	254
embryonic cell	1.33e-16	248
animal cell	2.00e-08	679
eukaryotic cell	2.00e-08	679
endodermal cell	3.37e-07	59
epithelial cell of lung	6.51e-07	19

Uber Anatomy

Ontology term	p-value	n
mesenchyme	6.55e-19	238
entire embryonic mesenchyme	6.55e-19	238
trunk	6.08e-12	216
foregut	6.37e-12	98
multi-tissue structure	7.09e-12	347
trunk region element	1.78e-11	107
segment of respiratory tract	2.79e-11	46
mixed endoderm/mesoderm-derived structure	1.95e-10	130
subdivision of digestive tract	3.12e-10	129
endodermal part of digestive tract	3.12e-10	129
endoderm-derived structure	7.40e-10	169
endoderm	7.40e-10	169
presumptive endoderm	7.40e-10	169
respiratory primordium	8.17e-10	38
endoderm of foregut	8.17e-10	38
subdivision of trunk	2.20e-09	113
primordium	2.77e-09	168
unilaminar epithelium	5.53e-09	138
digestive system	6.80e-09	155
digestive tract	6.80e-09	155
primitive gut	6.80e-09	155
epithelial tube	1.30e-08	118
trunk mesenchyme	1.53e-08	143
respiratory tract	2.10e-08	53
organ segment	4.92e-08	97
thoracic segment organ	1.52e-07	35
cell layer	1.64e-07	312
epithelium	1.91e-07	309
respiratory system	2.09e-07	72
compound organ	2.97e-07	69
thoracic cavity element	4.45e-07	34
thoracic cavity	4.45e-07	34
respiratory tract epithelium	6.51e-07	19
lung epithelium	6.51e-07	19

Disease

Ontology term	p-value	n
cancer	2.78e-27	235
disease of cellular proliferation	5.52e-26	239
cell type cancer	5.43e-20	143
carcinoma	8.54e-17	106
organ system cancer	3.04e-11	137
hematologic cancer	1.64e-08	51
immune system cancer	1.64e-08	51
myeloid leukemia	7.31e-07	31
leukemia	8.16e-07	39

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
BCLAF1#9774	2	10.8263238050609	0.0120220381643258	0.0436416282184227
BRCA1#672	2	10.0921153216119	0.013771396990026	0.048460895927805
CCNT2#905	4	6.33620157696263	0.000620310058721564	0.00511282157863006
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.010626485539454
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00995031291682237
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.0101273002735781
ELK4#2005	3	12.176761243851	0.000891263257762061	0.00663548926271827
ETS1#2113	3	7.29657069165175	0.0040085737751139	0.0191971495093141
GABPB1#2553	4	7.06768383618217	0.000400687686442317	0.00389749662702329
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185562850802807
HMGN3#9324	3	6.13391079251294	0.00664069668332472	0.0282861340556201
MAX#4149	3	4.83941663175534	0.0131573713783684	0.0465921645605877
MEF2A#4205	3	14.057423182233	0.000583003885418661	0.00488552858775893
MXI1#4601	3	7.47117872156947	0.00374131473855096	0.0186225893613346
MYC#4609	4	5.2222818716094	0.00134430939527274	0.00885626246974638
PAX5#5079	3	5.00217414838337	0.0119653317478641	0.0434735530497539
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00794392210606986
SP2#6668	2	13.0767652469223	0.00833003653661494	0.0328009910586106
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321269408782133
TAF7#6879	3	8.57480205369294	0.0025005543351524	0.0140262846666836
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0243506076157009
TCF7L2#6934	3	8.07763242235301	0.00297838168583462	0.0158566144103013
TFAP2C#7022	3	8.10692145739517	0.00294701173986644	0.015714436796687
THAP1#55145	2	15.6845723014257	0.00584046967835792	0.0262421619660137
USF1#7391	4	6.36149927720796	0.000610501139914083	0.00506998477667676
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106617503532146
ZBTB33#10009	2	15.8323625149906	0.00573424893032464	0.0258349175632706
ZBTB7A#51341	3	5.51393198090692	0.00903835282108109	0.0342248841695692
ZNF143#7702	4	13.5008765522279	3.00867915035614e-05	0.000619647883620676

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.