Coexpression cluster:C2605

Full id: C2605_Reticulocytes_liver_Hepatocyte_retina_left_heart_gastrointestinal

Phase1 CAGE Peaks

Hg19::chr1:95582881..95582994,+	p1@TMEM56
Hg19::chr1:95583232..95583264,+	p3@RWDD3 p3@TMEM56
Hg19::chr3:142682505..142682521,-	p2@PAQR9
Hg19::chr7:100239132..100239196,-	p3@TFR2

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:0004998	transferrin receptor activity	0.00865393104790558

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>

---

Uber Anatomy

Ontology term	p-value	n
adult organism	4.54e-49	115
neural plate	6.18e-25	86
presumptive neural plate	6.18e-25	86
neural tube	3.25e-24	57
neural rod	3.25e-24	57
future spinal cord	3.25e-24	57
neural keel	3.25e-24	57
central nervous system	5.92e-23	82
regional part of nervous system	7.18e-23	94
nervous system	7.18e-23	94
neurectoderm	1.25e-22	90
brain	3.65e-22	69
future brain	3.65e-22	69
regional part of brain	7.73e-20	59
anterior neural tube	9.65e-20	42
regional part of forebrain	1.42e-19	41
forebrain	1.42e-19	41
future forebrain	1.42e-19	41
pre-chordal neural plate	5.59e-18	61
telencephalon	1.66e-17	34
gray matter	3.31e-17	34
brain grey matter	3.31e-17	34
head	4.85e-17	123
regional part of telencephalon	6.22e-17	33
cerebral hemisphere	7.45e-17	32
anterior region of body	1.63e-16	129
craniocervical region	1.63e-16	129
ectoderm-derived structure	8.21e-16	169
multi-tissue structure	1.01e-15	347
ectoderm	1.00e-14	173
presumptive ectoderm	1.00e-14	173
regional part of cerebral cortex	9.23e-14	22
cerebral cortex	5.16e-13	25
pallium	5.16e-13	25
neocortex	1.19e-12	20
organ part	5.88e-12	219
anatomical cluster	5.01e-10	286
subdivision of digestive tract	5.89e-10	129
endodermal part of digestive tract	5.89e-10	129
digestive system	9.46e-10	155
digestive tract	9.46e-10	155
primitive gut	9.46e-10	155
organism subdivision	1.59e-08	365
organ	2.31e-08	511
anatomical conduit	4.17e-08	241
mixed endoderm/mesoderm-derived structure	7.19e-08	130
endoderm-derived structure	7.95e-08	169
endoderm	7.95e-08	169
presumptive endoderm	7.95e-08	169
tube	8.93e-08	194
epithelium	3.98e-07	309
cell layer	9.97e-07	312

Disease

Ontology term	p-value	n
carcinoma	5.91e-13	106
cell type cancer	8.25e-12	143
cancer	1.36e-07	235
disease of cellular proliferation	2.50e-07	239

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
CCNT2#905	4	6.33620157696263	0.000620310058721564	0.00512617203852045
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00997621264172694
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186250610477914
HMGN3#9324	3	6.13391079251294	0.00664069668332472	0.0283011393499449
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322558402976545
ZBTB7A#51341	3	5.51393198090692	0.00903835282108109	0.0342509626371875

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.