Coexpression cluster:C4005

Full id: C4005_small_colon_acute_Burkitt_Intestinal_renal_mesenchymal

Phase1 CAGE Peaks

Hg19::chr1:9129598..9129610,-	p3@SLC2A5
Hg19::chr1:9129614..9129619,-	p6@SLC2A5
Hg19::chr1:9129631..9129664,-	p2@SLC2A5

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

---

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>cell_data<br>uberon_data<br><br>

---

Cell Type

Ontology term	p-value	n
lymphocyte of B lineage	4.29e-10	24
pro-B cell	4.29e-10	24
fat cell	1.07e-07	15

Uber Anatomy

Ontology term	p-value	n
adult organism	2.33e-31	115
neural tube	4.47e-25	57
neural rod	4.47e-25	57
future spinal cord	4.47e-25	57
neural keel	4.47e-25	57
regional part of brain	5.18e-20	59
regional part of forebrain	8.72e-19	41
forebrain	8.72e-19	41
future forebrain	8.72e-19	41
anterior neural tube	6.45e-18	42
telencephalon	1.65e-16	34
gray matter	1.72e-16	34
brain grey matter	1.72e-16	34
brain	2.20e-16	69
future brain	2.20e-16	69
central nervous system	6.06e-16	82
regional part of telencephalon	6.11e-16	33
cerebral hemisphere	3.94e-15	32
neural plate	5.53e-14	86
presumptive neural plate	5.53e-14	86
neurectoderm	2.09e-13	90
regional part of nervous system	4.67e-13	94
nervous system	4.67e-13	94
regional part of cerebral cortex	4.28e-11	22
cerebral cortex	7.96e-11	25
pallium	7.96e-11	25
neocortex	8.42e-10	20
pre-chordal neural plate	3.44e-09	61
posterior neural tube	2.24e-08	15
chordal neural plate	2.24e-08	15
tissue	1.43e-07	787
nucleus of brain	1.90e-07	9
neural nucleus	1.90e-07	9
basal ganglion	2.29e-07	9
nuclear complex of neuraxis	2.29e-07	9
aggregate regional part of brain	2.29e-07	9
collection of basal ganglia	2.29e-07	9
cerebral subcortex	2.29e-07	9
segmental subdivision of nervous system	6.84e-07	13

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
BATF#10538	3	24.3578017923036	6.91705216281876e-05	0.00109972600218089
BCL11A#53335	3	28.3694551036071	4.37778126761649e-05	0.000778099213425116
BCL3#602	3	34.5471028037383	2.42397750207122e-05	0.000527412054872534
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0279801590265632
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00915828131347991
IRF4#3662	3	21.9145126867441	9.49854535978121e-05	0.00136792412966105
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186773476329452
MEF2A#4205	3	18.7432309096441	0.000151824390562247	0.00195083507946979
MEF2C#4208	3	41.3113544926241	1.41744912101957e-05	0.000340471409269004
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269857930738612
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173087048443791
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00883106568062126
REST#5978	3	9.65002871612802	0.00111263624711459	0.007685866592526
SP1#6667	3	5.6983813781409	0.00540396270171217	0.024684414826982
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109171838871223
SRF#6722	3	13.7971782621678	0.000380661502580019	0.003754453363675
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00629810047883878

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.