Coexpression cluster:C3315

Full id: C3315_neuroblastoma_hepatoma_rhabdomyosarcoma_testicular_maxillary_pancreatic_extraskeletal

Phase1 CAGE Peaks

Hg19::chr12:64798095..64798162,+	p4@XPOT
Hg19::chr12:64798164..64798192,+	p3@XPOT
Hg19::chr12:64798203..64798275,+	p2@XPOT

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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No GOStat results

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><br>uberon_data<br>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
body cavity or lining	1.22e-07	49
body cavity	4.52e-07	46

Disease

Ontology term	p-value	n
disease of cellular proliferation	3.24e-49	239
cancer	8.48e-49	235
cell type cancer	8.14e-32	143
organ system cancer	9.27e-24	137
carcinoma	2.12e-22	106
germ cell and embryonal cancer	3.28e-09	22
germ cell cancer	3.28e-09	22
disease of anatomical entity	1.70e-08	39
hematologic cancer	1.93e-07	51
immune system cancer	1.93e-07	51

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	3	22.4631745260087	8.81932387510763e-05	0.00129383532264695
BCLAF1#9774	3	21.6526476101218	9.8473954032885e-05	0.00138980017368115
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189487008070736
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.0017136443054184
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324135004284475
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00436166478388977
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321007945890533
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319527423605434
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460672584445828
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00255256428849294
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167065033590423
ESR1#2099	3	30.7686032961545	3.43136389821584e-05	0.000674511978478758
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00760743633390137
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00895610443686176
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00580067323597349
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0153746803510458
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00433008145785337
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108454151282705
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127763619725858
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156345206690337
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186049374880034
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00719059096443748
MYC#4609	3	5.2222818716094	0.00702084375574015	0.029358179892927
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.026892750497818
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00470007369215117
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172493296929968
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00880464051432667
REST#5978	3	9.65002871612802	0.00111263624711459	0.0076595225767847
SETDB1#9869	3	40.3200261780105	1.52461559299059e-05	0.000358221210160505
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275804944006794
SIX5#147912	3	17.086715355459	0.000200406054632501	0.00239229716993528
SP1#6667	3	5.6983813781409	0.00540396270171217	0.02457478274859
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00374208458847464
TAL1#6886	3	29.8686166774402	3.75103522793067e-05	0.000719079236728801
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00247647253018341
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.0061391230741393
THAP1#55145	3	31.3691446028513	3.23800758564397e-05	0.000645493938226896
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189740078298184
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00420837236052861
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328349033312146
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.0038814058500774

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.