Coexpression cluster:C3655

Full id: C3655_mature_optic_corpus_spinal_globus_medulla_substantia

Phase1 CAGE Peaks

Hg19::chr17:48785216..48785291,-	p1@ANKRD40
Hg19::chr1:149982554..149982573,-	p3@OTUD7B
Hg19::chr8:27468717..27468788,-	p3@CLU

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:0016235	aggresome	0.00953656411554144
GO:0016579	protein deubiquitination	0.00953656411554144
GO:0043124	negative regulation of I-kappaB kinase/NF-kappaB cascade	0.00953656411554144
GO:0016234	inclusion body	0.00953656411554144
GO:0031018	endocrine pancreas development	0.00953656411554144
GO:0031016	pancreas development	0.0132444480846854
GO:0048523	negative regulation of cellular process	0.020411819014579
GO:0048519	negative regulation of biological process	0.020411819014579
GO:0006958	complement activation, classical pathway	0.0238298294633898
GO:0002455	humoral immune response mediated by circulating immunoglobulin	0.0238298294633898
GO:0035270	endocrine system development	0.0238298294633898
GO:0006956	complement activation	0.0238298294633898
GO:0002541	activation of plasma proteins during acute inflammatory response	0.0238298294633898
GO:0045597	positive regulation of cell differentiation	0.0250859676778148
GO:0016064	immunoglobulin mediated immune response	0.0250859676778148
GO:0019724	B cell mediated immunity	0.0250859676778148
GO:0048471	perinuclear region of cytoplasm	0.0250859676778148
GO:0051094	positive regulation of developmental process	0.0250859676778148
GO:0002253	activation of immune response	0.0250859676778148
GO:0002449	lymphocyte mediated immunity	0.0250859676778148
GO:0006959	humoral immune response	0.0250859676778148
GO:0002250	adaptive immune response	0.0250859676778148
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0250859676778148
GO:0002443	leukocyte mediated immunity	0.0250859676778148
GO:0002526	acute inflammatory response	0.0250859676778148
GO:0050778	positive regulation of immune response	0.0252832945456699
GO:0002684	positive regulation of immune system process	0.0252832945456699
GO:0050776	regulation of immune response	0.0256392892352884
GO:0002682	regulation of immune system process	0.0256392892352884
GO:0009968	negative regulation of signal transduction	0.0256392892352884
GO:0051240	positive regulation of multicellular organismal process	0.0256392892352884
GO:0043122	regulation of I-kappaB kinase/NF-kappaB cascade	0.0256392892352884
GO:0002252	immune effector process	0.0256392892352884
GO:0045087	innate immune response	0.0256392892352884
GO:0048667	neuron morphogenesis during differentiation	0.0256392892352884
GO:0006979	response to oxidative stress	0.0256392892352884
GO:0048812	neurite morphogenesis	0.0256392892352884
GO:0000904	cellular morphogenesis during differentiation	0.0256392892352884
GO:0031175	neurite development	0.0256392892352884
GO:0004221	ubiquitin thiolesterase activity	0.0256392892352884
GO:0004843	ubiquitin-specific protease activity	0.0256392892352884
GO:0007249	I-kappaB kinase/NF-kappaB cascade	0.0256392892352884
GO:0019783	small conjugating protein-specific protease activity	0.0256392892352884
GO:0045595	regulation of cell differentiation	0.0259559796898568
GO:0048666	neuron development	0.0271376199582455
GO:0006916	anti-apoptosis	0.0292989543931793
GO:0016790	thiolester hydrolase activity	0.0306942946902211
GO:0032990	cell part morphogenesis	0.0323298184570564
GO:0048858	cell projection morphogenesis	0.0323298184570564
GO:0030030	cell projection organization and biogenesis	0.0323298184570564
GO:0030182	neuron differentiation	0.0326252427686447
GO:0043066	negative regulation of apoptosis	0.0339849946966792
GO:0043069	negative regulation of programmed cell death	0.0339849946966792
GO:0008284	positive regulation of cell proliferation	0.0339849946966792
GO:0050793	regulation of developmental process	0.0339849946966792
GO:0048699	generation of neurons	0.0342236829839282
GO:0022008	neurogenesis	0.0363912961601846
GO:0051239	regulation of multicellular organismal process	0.0378030291928459
GO:0006954	inflammatory response	0.0390324614353745
GO:0008234	cysteine-type peptidase activity	0.0394324299568541
GO:0007243	protein kinase cascade	0.0487188432564292

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><br>

---

Uber Anatomy

Ontology term	p-value	n
adult organism	2.86e-48	115
neural tube	1.08e-30	57
neural rod	1.08e-30	57
future spinal cord	1.08e-30	57
neural keel	1.08e-30	57
regional part of nervous system	1.89e-29	94
nervous system	1.89e-29	94
neural plate	3.57e-28	86
presumptive neural plate	3.57e-28	86
central nervous system	1.08e-27	82
neurectoderm	4.76e-27	90
brain	5.70e-27	69
future brain	5.70e-27	69
regional part of brain	4.92e-26	59
anterior neural tube	7.97e-22	42
regional part of forebrain	2.36e-21	41
forebrain	2.36e-21	41
future forebrain	2.36e-21	41
ectoderm-derived structure	5.37e-21	169
head	1.02e-20	123
ectoderm	1.33e-20	173
presumptive ectoderm	1.33e-20	173
anterior region of body	1.99e-20	129
craniocervical region	1.99e-20	129
pre-chordal neural plate	2.43e-19	61
anatomical cluster	2.15e-18	286
anatomical conduit	2.44e-18	241
telencephalon	2.72e-18	34
gray matter	2.97e-18	34
brain grey matter	2.97e-18	34
organism subdivision	7.11e-18	365
regional part of telencephalon	1.15e-17	33
cerebral hemisphere	5.75e-17	32
multi-cellular organism	2.54e-16	659
multi-tissue structure	1.01e-14	347
epithelium	1.39e-14	309
cell layer	1.86e-14	312
tube	4.04e-14	194
cerebral cortex	8.76e-13	25
pallium	8.76e-13	25
anatomical system	1.01e-12	625
anatomical group	1.18e-12	626
regional part of cerebral cortex	8.94e-12	22
embryo	1.77e-11	612
neocortex	1.22e-10	20
embryonic structure	3.42e-10	605
developing anatomical structure	3.42e-10	605
organ part	3.57e-10	219
organ	3.75e-10	511
posterior neural tube	5.46e-10	15
chordal neural plate	5.46e-10	15
germ layer	6.61e-10	604
embryonic tissue	6.61e-10	604
presumptive structure	6.61e-10	604
epiblast (generic)	6.61e-10	604
segmental subdivision of nervous system	7.97e-09	13
segmental subdivision of hindbrain	3.74e-08	12
hindbrain	3.74e-08	12
presumptive hindbrain	3.74e-08	12
nucleus of brain	4.79e-07	9
neural nucleus	4.79e-07	9
basal ganglion	6.84e-07	9
nuclear complex of neuraxis	6.84e-07	9
aggregate regional part of brain	6.84e-07	9
collection of basal ganglia	6.84e-07	9
cerebral subcortex	6.84e-07	9

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
BCLAF1#9774	2	14.4350984067479	0.00620114743554613	0.0273809511275949
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115140515925214
ELK4#2005	2	10.823787772312	0.0109128471951648	0.0401906639472394
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167331299208258
GATA3#2625	2	18.1576775714707	0.00394454681927962	0.018946995596686
MEF2C#4208	2	27.5409029950827	0.00172911993836969	0.0106472234681559
RXRA#6256	2	13.3830780927555	0.00719643442946573	0.0298261206944312
SIX5#147912	2	11.391143570306	0.00987382008142903	0.0370726163173845

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.