Coexpression cluster:C1675

Full id: C1675_Hodgkin_Burkitt_retinoblastoma_Reticulocytes_granulocyte_diffuse_MCF7

Phase1 CAGE Peaks

Hg19::chr12:53662049..53662061,+	p2@ESPL1
Hg19::chr12:53662073..53662105,+	p1@ESPL1
Hg19::chr16:89883015..89883088,-	p1@FANCA
Hg19::chr19:48673552..48673578,-	p2@LIG1
Hg19::chr21:47743719..47743792,-	p1@C21orf58

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:0051301	cell division	0.00408715906915419
GO:0045875	negative regulation of sister chromatid cohesion	0.00408715906915419
GO:0007063	regulation of sister chromatid cohesion	0.00408715906915419
GO:0045842	positive regulation of mitotic metaphase/anaphase transition	0.00408715906915419
GO:0051293	establishment of spindle localization	0.00408715906915419
GO:0051653	spindle localization	0.00408715906915419
GO:0040001	establishment of mitotic spindle localization	0.00408715906915419
GO:0003910	DNA ligase (ATP) activity	0.00474459431445905
GO:0006281	DNA repair	0.00474459431445905
GO:0003909	DNA ligase activity	0.00476807151383685
GO:0006974	response to DNA damage stimulus	0.00506629389735859
GO:0009719	response to endogenous stimulus	0.0064670891858124
GO:0007062	sister chromatid cohesion	0.00660116780290485
GO:0030071	regulation of mitotic metaphase/anaphase transition	0.00715063354999629
GO:0007091	mitotic metaphase/anaphase transition	0.00715063354999629
GO:0045840	positive regulation of mitosis	0.00715063354999629
GO:0016886	ligase activity, forming phosphoric ester bonds	0.00785121375196704
GO:0007049	cell cycle	0.0107858894254426
GO:0051656	establishment of organelle localization	0.0114369722282121
GO:0045787	positive regulation of progression through cell cycle	0.0114369722282121
GO:0000070	mitotic sister chromatid segregation	0.0125614912332567
GO:0000819	sister chromatid segregation	0.0125614912332567
GO:0051640	organelle localization	0.0134980059960521
GO:0000910	cytokinesis	0.0134980059960521
GO:0006950	response to stress	0.0163545176936061
GO:0006259	DNA metabolic process	0.0164194544395607
GO:0007059	chromosome segregation	0.0208051301178182
GO:0005634	nucleus	0.0218631855041171
GO:0007088	regulation of mitosis	0.0219915913189527
GO:0000226	microtubule cytoskeleton organization and biogenesis	0.0323303903291635
GO:0005813	centrosome	0.0395379803144608
GO:0005815	microtubule organizing center	0.0436237898276382

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
epithelial cell	8.73e-16	254
animal cell	2.60e-10	679
eukaryotic cell	2.60e-10	679
migratory neural crest cell	1.15e-07	41
embryonic cell	6.48e-07	248
neural cell	7.05e-07	25

Disease

Ontology term	p-value	n
cancer	1.82e-41	235
disease of cellular proliferation	9.02e-40	239
hematologic cancer	2.27e-23	51
immune system cancer	2.27e-23	51
organ system cancer	7.40e-23	137
leukemia	6.35e-19	39
cell type cancer	8.15e-19	143
carcinoma	3.90e-15	106
myeloid leukemia	1.87e-14	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)
{{{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
CCNT2#905	5	6.33620157696263	9.78880505817628e-05	0.00138903941775934
CHD2#1106	5	10.3440228341169	8.43981772346334e-06	0.000230082517154996
CTBP2#1488	2	25.0868001357313	0.00246143859967838	0.0138462881564048
CTCF#10664	4	4.28820509846002	0.00515201558824328	0.023923852030614
E2F1#1869	5	4.90738921487932	0.000351281809925646	0.00352391902284358
E2F4#1874	5	12.6680603152844	3.06319883889696e-06	0.000103365888056724
E2F6#1876	5	5.01715573169739	0.000314497859929779	0.00322523978723548
EGR1#1958	5	4.98817909481014	0.000323739800059071	0.00330508904969397
ELF1#1997	5	4.25809795880754	0.000714241693977684	0.00572703940708909
ETS1#2113	3	5.8372565533214	0.00925327904563143	0.0349677320348338
FOS#2353	4	7.19836424711553	0.000694785845338251	0.00559509128701377
IRF1#3659	5	7.6371637535639	3.84754333311872e-05	0.000723503021547689
MXI1#4601	4	7.96925730300744	0.000466854638007017	0.00429395257937603
NFYA#4800	4	14.7404645598644	4.14733626928016e-05	0.000752116083742577
NFYB#4801	4	13.4078346028292	6.03169250119439e-05	0.00099125717251336
NRF1#4899	3	7.32616766862654	0.00483968981711754	0.0226863718496382
PAX5#5079	5	6.66956553117783	7.57493746384605e-05	0.00116960214930014
PBX3#5090	4	17.5316101493953	2.08739444052064e-05	0.000460704539250919
RAD21#5885	3	6.2130203372738	0.00775105506881164	0.0318868885780761
SIN3A#25942	5	5.40888472681514	0.000215952267165727	0.00247817150099125
SIX5#147912	3	10.2520292132754	0.00183229106867769	0.0108482226146049
SMARCB1#6598	3	10.9516294686944	0.00151187284834318	0.00965090693772468
SMARCC1#6599	2	17.4653437278526	0.00500803738519939	0.0233768846193277
SMC3#9126	3	9.0269597069597	0.00265096444946755	0.0146349548650989
SP1#6667	5	5.6983813781409	0.00016639184371255	0.00204084530422725
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135205513807863
TAL1#6886	2	11.9474466709761	0.010475778180992	0.0388026598611371
TFAP2A#7020	3	9.91118062382697	0.00202154697751128	0.0117443591691773
TFAP2C#7022	3	6.48553716591613	0.00685895151794	0.0290546354728102
YY1#7528	5	4.91117074985386	0.0003499314082136	0.00352527118186748
ZNF143#7702	3	8.10052593133674	0.00362487051209098	0.01832774261291
ZNF263#10127	4	6.57747330960854	0.000987510323790016	0.00709023722716249

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.