Coexpression cluster:C4496

Full id: C4496_oral_chronic_small_Hep2_cervical_choriocarcinoma_synovial

Phase1 CAGE Peaks

Hg19::chr5:34915771..34915791,+	p3@BRIX1
Hg19::chr5:34915805..34915847,+	p1@BRIX1
Hg19::chr5:37371163..37371231,-	p1@NUP155

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:0017056	structural constituent of nuclear pore	0.00989049805722359
GO:0065002	intracellular protein transport across a membrane	0.014257730965608
GO:0051028	mRNA transport	0.014257730965608
GO:0005643	nuclear pore	0.014257730965608
GO:0050658	RNA transport	0.014257730965608
GO:0051236	establishment of RNA localization	0.014257730965608
GO:0050657	nucleic acid transport	0.014257730965608
GO:0006403	RNA localization	0.014257730965608
GO:0046930	pore complex	0.014257730965608
GO:0015931	nucleobase, nucleoside, nucleotide and nucleic acid transport	0.014257730965608
GO:0044453	nuclear membrane part	0.014257730965608
GO:0031965	nuclear membrane	0.0157440581319069
GO:0006913	nucleocytoplasmic transport	0.0157440581319069
GO:0051169	nuclear transport	0.0157440581319069
GO:0005635	nuclear envelope	0.0182738726009655
GO:0006886	intracellular protein transport	0.0467149417167079
GO:0031967	organelle envelope	0.0489815141881549
GO:0031975	envelope	0.0489815141881549

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	1.06e-08	253
nucleate cell	3.10e-08	55
lymphocyte	1.32e-07	53
common lymphoid progenitor	1.32e-07	53
lymphoid lineage restricted progenitor cell	2.71e-07	52

Uber Anatomy

Ontology term	p-value	n
larynx	1.24e-07	9

Disease

Ontology term	p-value	n
cancer	5.64e-66	235
disease of cellular proliferation	2.49e-64	239
cell type cancer	3.23e-44	143
carcinoma	4.99e-37	106
organ system cancer	1.87e-25	137
hematologic cancer	1.35e-15	51
immune system cancer	1.35e-15	51
leukemia	4.78e-13	39
myeloid leukemia	1.65e-10	31
disease of anatomical entity	6.01e-07	39
germ cell and embryonal cancer	6.65e-07	22
germ cell cancer	6.65e-07	22
respiratory system cancer	8.36e-07	16

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	14.4350984067479	0.00620114743554613	0.0273971672668472
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190870189225055
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327147032201819
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00438549901768152
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323899909367025
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0322083740843741
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464437050543617
ELK4#2005	3	16.235681658468	0.000233604395574599	0.0025622148151035
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00764435816848451
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.015468751975409
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00435472450141795
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0109061390431748
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128604677072235
JUNB#3726	2	20.4070884398808	0.00313146219943874	0.0164551839319337
KAT2A#2648	1	205.363333333333	0.00486154522073778	0.022755116806733
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187241309699834
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00722402871220345
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295677205131556
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.027058605826598
NR3C1#2908	2	9.98201555411536	0.0127847436554717	0.0460708661456701
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173530773868711
REST#5978	3	9.65002871612802	0.00111263624711459	0.00770421116570978
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00486121843400306
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277942246470458
SIX5#147912	3	17.086715355459	0.000200406054632501	0.00240245729336132
SMC3#9126	2	10.0299552299552	0.012665637976747	0.0457806660432436
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247623929713986
SP2#6668	2	17.4356869958964	0.00427356848176974	0.0203282573632515
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.010934228177914
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00376084634073925
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00631321262279294
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00616495243858555
TFAP2A#7020	2	11.0124229153633	0.0105499065521556	0.0390329350432402
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00618181006074827
THAP1#55145	3	31.3691446028513	3.23800758564397e-05	0.000648588941766534
TRIM28#10155	3	18.5905250452625	0.000155596929725528	0.00197741393813633
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330875269072289
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109922394279632

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.