Coexpression cluster:C4408

Full id: C4408_fibrous_Reticulocytes_carcinoid_testicular_iPS_alveolar_teratocarcinoma

Phase1 CAGE Peaks

Hg19::chr4:37962018..37962027,+	p1@PTTG2
Hg19::chr5:159848807..159848847,+	p2@PTTG1
Hg19::chr5:159848854..159848878,+	p1@PTTG1

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
1.99497924496294e-05	0.00420940620687181	2	128	Cell cycle (KEGG):04110
1.58091305570944e-05	0.00420940620687181	2	114	Oocyte meiosis (KEGG):04114
9.83008350895251e-06	0.00420940620687181	2	90	Cell cycle (Wikipathways):WP179
0.00014649401603791	0.0231826780379993	2	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:0051276	chromosome organization and biogenesis	0.0121754551432509
GO:0006259	DNA metabolic process	0.0295510600856273
GO:0006996	organelle organization and biogenesis	0.0295510600856273
GO:0004869	cysteine protease inhibitor activity	0.0295510600856273
GO:0007059	chromosome segregation	0.0340107387499807

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><br>disease_data<br>

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Cell Type

Ontology term	p-value	n
animal cell	4.40e-25	679
eukaryotic cell	4.40e-25	679
epithelial cell	6.21e-22	253
native cell	6.06e-15	722
embryonic cell	5.81e-14	250
ectodermal cell	4.15e-08	72
migratory neural crest cell	1.69e-07	41
neurectodermal cell	2.51e-07	59
non-terminally differentiated cell	4.56e-07	106
somatic cell	7.74e-07	588

Disease

Ontology term	p-value	n
cancer	7.55e-38	235
disease of cellular proliferation	1.20e-36	239
cell type cancer	4.63e-18	143
organ system cancer	1.11e-17	137
carcinoma	4.20e-15	106
hematologic cancer	4.23e-14	51
immune system cancer	4.23e-14	51
leukemia	1.00e-09	39
myeloid leukemia	3.25e-07	31

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)
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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
GATA3#2625	2	18.1576775714707	0.00394454681927962	0.0189565859220847
NANOG#79923	2	19.4965189873418	0.00342725564850102	0.0174578916584792

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.