Coexpression cluster:C1197

Full id: C1197_hepatoma_Hepatocyte_liver_argyrophil_hepatocellular_gastrointestinal_mesothelioma

Phase1 CAGE Peaks

Hg19::chr14:23445892..23445897,-	p17@AJUBA
Hg19::chr14:23445927..23445936,-	p15@AJUBA
Hg19::chr16:52417646..52417654,-	p@chr16:52417646..52417654 -
Hg19::chr2:73248062..73248100,-	p21@SFXN5
Hg19::chr5:147209673..147209678,-	p@chr5:147209673..147209678 -
Hg19::chr6:50061315..50061323,+	p1@ENST00000415106
Hg19::chr9:116840728..116840744,-	p2@AMBP

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

---

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

---

GO ID	GO name	FDR corrected p-value
GO:0030568	plasmin inhibitor activity	0.00260500985625729
GO:0046904	calcium oxalate binding	0.00260500985625729
GO:0019862	IgA binding	0.00260500985625729
GO:0019855	calcium channel inhibitor activity	0.00260500985625729
GO:0046329	negative regulation of JNK cascade	0.00260500985625729
GO:0042167	heme catabolic process	0.00260500985625729
GO:0030304	trypsin inhibitor activity	0.00260500985625729
GO:0046149	pigment catabolic process	0.00260500985625729
GO:0006787	porphyrin catabolic process	0.00347324422754211
GO:0033015	tetrapyrrole catabolic process	0.00347324422754211
GO:0050777	negative regulation of immune response	0.00496141229839008
GO:0002683	negative regulation of immune system process	0.00496141229839008
GO:0008200	ion channel inhibitor activity	0.00496141229839008
GO:0016248	channel inhibitor activity	0.00496141229839008
GO:0005246	calcium channel regulator activity	0.0050936416448709
GO:0019865	immunoglobulin binding	0.00694536373294039
GO:0046328	regulation of JNK cascade	0.00767588960040256
GO:0042168	heme metabolic process	0.00767588960040256
GO:0018298	protein-chromophore linkage	0.00767588960040256
GO:0051241	negative regulation of multicellular organismal process	0.00868055438216479
GO:0006778	porphyrin metabolic process	0.00991990324056249
GO:0033013	tetrapyrrole metabolic process	0.0108678033134421
GO:0016247	channel regulator activity	0.0108678033134421
GO:0042440	pigment metabolic process	0.012149734272869
GO:0051187	cofactor catabolic process	0.0138837746380827
GO:0019748	secondary metabolic process	0.0141501450216093
GO:0006826	iron ion transport	0.0146535844609547
GO:0007254	JNK cascade	0.01611153515917
GO:0031098	stress-activated protein kinase signaling pathway	0.0162732133377396
GO:0007565	female pregnancy	0.018734537648372
GO:0050776	regulation of immune response	0.0206109159829187
GO:0002682	regulation of immune system process	0.0206109159829187
GO:0032403	protein complex binding	0.0206109159829187
GO:0000041	transition metal ion transport	0.0206109159829187
GO:0009968	negative regulation of signal transduction	0.0206109159829187
GO:0046483	heterocycle metabolic process	0.0250383882725595
GO:0000165	MAPKKK cascade	0.0281013347524844
GO:0042803	protein homodimerization activity	0.0288177222531866
GO:0004867	serine-type endopeptidase inhibitor activity	0.0298515414307917
GO:0006810	transport	0.0406471491569161
GO:0015674	di-, tri-valent inorganic cation transport	0.0406471491569161
GO:0004866	endopeptidase inhibitor activity	0.0406471491569161
GO:0051234	establishment of localization	0.0406471491569161
GO:0030414	protease inhibitor activity	0.0418333476446704
GO:0051239	regulation of multicellular organismal process	0.042588301530179
GO:0020037	heme binding	0.0427626175573073
GO:0046906	tetrapyrrole binding	0.0427626175573073
GO:0051179	localization	0.0427626175573073
GO:0022414	reproductive process	0.043047415010481
GO:0051704	multi-organism process	0.046040255562797
GO:0051186	cofactor metabolic process	0.046486109454568
GO:0042802	identical protein binding	0.0477151929368722
GO:0046983	protein dimerization activity	0.0477151929368722
GO:0007243	protein kinase cascade	0.0481040101179392

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>

---

Cell Type

Ontology term	p-value	n
metabolising cell	1.39e-47	12
endopolyploid cell	1.39e-47	12
parenchymal cell	1.39e-47	12
polyploid cell	1.39e-47	12
hepatocyte	1.39e-47	12
endodermal cell	2.31e-15	58

Uber Anatomy

Ontology term	p-value	n
hepatic diverticulum	1.70e-52	22
liver primordium	1.70e-52	22
digestive tract diverticulum	3.62e-50	23
liver	2.27e-49	19
digestive gland	2.27e-49	19
liver bud	2.27e-49	19
epithelial sac	4.52e-46	25
epithelium of foregut-midgut junction	4.52e-46	25
anatomical boundary	4.52e-46	25
hepatobiliary system	4.52e-46	25
foregut-midgut junction	4.52e-46	25
septum transversum	4.52e-46	25
sac	2.93e-44	26
exocrine gland	6.47e-30	31
exocrine system	6.47e-30	31
gut epithelium	7.62e-30	54
endocrine gland	2.18e-26	35
abdomen element	4.97e-25	54
abdominal segment element	4.97e-25	54
abdominal segment of trunk	2.16e-22	60
abdomen	2.16e-22	60
endocrine system	2.63e-20	45
endo-epithelium	3.86e-19	82
gland	8.75e-19	59
trunk region element	9.99e-13	101
subdivision of digestive tract	1.08e-12	118
foregut	2.18e-12	87
subdivision of trunk	2.48e-11	112
mesenchyme	9.96e-11	160
entire embryonic mesenchyme	9.96e-11	160
trunk mesenchyme	2.73e-10	122
digestive system	4.84e-10	145
digestive tract	4.84e-10	145
primitive gut	4.84e-10	145
unilaminar epithelium	6.97e-10	148
endoderm-derived structure	5.98e-09	160
endoderm	5.98e-09	160
presumptive endoderm	5.98e-09	160
immaterial anatomical entity	7.10e-09	117
epithelial tube	7.10e-09	117
trunk	2.89e-08	199

Disease

Ontology term	p-value	n
disease of anatomical entity	1.66e-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

---

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

---

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
CEBPB#1051	4	4.55494150047132	0.00632108033306846	0.0275299127983877
EP300#2033	7	6.7739417262232	1.52695018318475e-06	5.86082874610924e-05
FOSL2#2355	3	7.25580025909787	0.00602077509384975	0.0269849682442097
FOXA1#3169	6	9.49835978518753	3.4851329158676e-06	0.000115881501623781
FOXA2#3170	6	21.1118260737131	3.02035985915038e-08	2.04700430454125e-06
HDAC2#3066	5	9.58258588330447	4.24859153994197e-05	0.00076005250400822
HNF4A#3172	3	9.91383872698015	0.00247865482166154	0.0139228866196692
HNF4G#3174	3	12.3228953684772	0.00132445022199723	0.00879254110953275
MAFK#7975	3	11.6145999162128	0.00157162661744092	0.00996533982750971
TCF7L2#6934	4	6.15438660750705	0.00206467614813804	0.0119709494384827

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

---

This analysis result is provided for C0 - C305 clusters.