Coexpression cluster:C1332

Full id: C1332_lymphoma_Reticulocytes_chronic_embryonic_Renal_Hodgkin_Alveolar

Phase1 CAGE Peaks

Hg19::chr11:118966167..118966182,-	p1@H2AFX
Hg19::chr16:29802036..29802086,+	p1@KIF22
Hg19::chr19:36545781..36545828,+	p1@WDR62
Hg19::chr22:35796108..35796172,+	p1@MCM5
Hg19::chr22:42343092..42343107,-	p2@CENPM
Hg19::chr22:42343117..42343181,-	p1@CENPM

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:0044427	chromosomal part	0.000875186642580658
GO:0005694	chromosome	0.000875186642580658
GO:0000775	chromosome, pericentric region	0.00112284037717332
GO:0000279	M phase	0.0136644533982684
GO:0022403	cell cycle phase	0.015865546315125
GO:0005634	nucleus	0.019196970695774
GO:0000724	double-strand break repair via homologous recombination	0.0201244507432831
GO:0000725	recombinational repair	0.0201244507432831
GO:0022402	cell cycle process	0.0246058068434886
GO:0043232	intracellular non-membrane-bound organelle	0.0246058068434886
GO:0043228	non-membrane-bound organelle	0.0246058068434886
GO:0007049	cell cycle	0.0273338469233302
GO:0000776	kinetochore	0.0273338469233302
GO:0005657	replication fork	0.0273338469233302
GO:0003677	DNA binding	0.0273338469233302
GO:0006302	double-strand break repair	0.0273338469233302
GO:0006270	DNA replication initiation	0.0273338469233302
GO:0043231	intracellular membrane-bound organelle	0.0273338469233302
GO:0043227	membrane-bound organelle	0.0273338469233302
GO:0003684	damaged DNA binding	0.0328162701163738
GO:0044446	intracellular organelle part	0.0338266050298457
GO:0044422	organelle part	0.0338266050298457
GO:0006259	DNA metabolic process	0.0365414791603242
GO:0051327	M phase of meiotic cell cycle	0.0365414791603242
GO:0007126	meiosis	0.0365414791603242
GO:0051321	meiotic cell cycle	0.0365414791603242
GO:0008094	DNA-dependent ATPase activity	0.039664069222455
GO:0043229	intracellular organelle	0.039664069222455
GO:0043226	organelle	0.039664069222455
GO:0006996	organelle organization and biogenesis	0.0432719300434897

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
animal cell	1.15e-17	679
eukaryotic cell	1.15e-17	679
epithelial cell	2.88e-15	253
native cell	2.58e-13	722
embryonic cell	1.73e-08	250
migratory neural crest cell	2.90e-08	41
neurectodermal cell	6.44e-07	59
epithelial cell of nephron	6.94e-07	15
kidney cell	9.00e-07	17
kidney epithelial cell	9.00e-07	17

Uber Anatomy

Ontology term	p-value	n
nephron epithelium	6.94e-07	15
renal tubule	6.94e-07	15
nephron tubule	6.94e-07	15
nephron	6.94e-07	15
uriniferous tubule	6.94e-07	15
nephrogenic mesenchyme	6.94e-07	15

Disease

Ontology term	p-value	n
cancer	1.10e-31	235
disease of cellular proliferation	5.08e-30	239
hematologic cancer	1.36e-21	51
immune system cancer	1.36e-21	51
organ system cancer	2.90e-18	137
leukemia	3.67e-17	39
cell type cancer	2.10e-13	143
myeloid leukemia	7.34e-13	31
carcinoma	1.23e-11	106

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
BHLHE40#8553	2	14.9572711823258	0.0070165594845194	0.0296369188709747
CHD2#1106	4	6.89601522274457	0.00111539132013599	0.00765930397025989
E2F1#1869	6	4.90738921487932	7.15746523583771e-05	0.00112645948126229
E2F4#1874	6	12.6680603152844	2.41728555395527e-07	1.26800043179073e-05
E2F6#1876	6	5.01715573169739	6.26776799983417e-05	0.00102457258120939
EGR1#1958	5	4.15681591234178	0.00161796681886444	0.0101294111374765
ELF1#1997	6	4.25809795880754	0.000167722477628883	0.00205114377530245
ELK4#2005	3	8.11784082923401	0.00405611313418576	0.0194070184909853
FOS#2353	4	5.99863687259627	0.00189982371188635	0.0111821285305285
GATA1#2623	4	9.0402054292003	0.000392739784014487	0.00384093550919458
GTF2F1#2962	3	6.36983043837883	0.00806820819630316	0.0319131796626915
HEY1#23462	6	4.04011104310571	0.000229896855580751	0.00252925289160413
IRF1#3659	4	5.09144250237593	0.00353524076589381	0.0179431895003734
IRF3#3661	2	15.6606507371632	0.00641762098993253	0.027911960961461
MXI1#4601	6	9.9615716287593	1.02262624227062e-06	4.29959992417476e-05
NFKB1#4790	5	4.5733861868282	0.0010219625937113	0.00724299343950964
NFYA#4800	4	12.2837204665537	0.000119030250924586	0.00161593661462535
NFYB#4801	4	11.1731955023576	0.000172334334821877	0.00209894176028712
PAX5#5079	5	5.55797127598152	0.000397717619661286	0.00388525212606913
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0379929860192945
POU2F2#5452	5	7.58843671478544	8.70203885493171e-05	0.00129022180007128
RFX5#5993	3	6.02395541359755	0.00943790403633506	0.0356010134594141
SIN3A#25942	6	5.40888472681514	3.99207083571449e-05	0.000742260790477453
SP1#6667	6	5.6983813781409	2.91961319085282e-05	0.000608990377550386
SP2#6668	3	13.0767652469223	0.00102434039793732	0.0072583680589033
TAF1#6872	6	3.34304628574529	0.000716247428463562	0.00572597712655435
TFAP2C#7022	4	7.20615240657348	0.000942141368921255	0.00681745322724084
USF1#7391	5	5.3012493976733	0.000500332754985889	0.0044103859383838
YY1#7528	6	4.91117074985386	7.12445972864136e-05	0.00112363553246689
ZEB1#6935	3	8.44421600877193	0.00362384381073359	0.0183340901879187

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.