Coexpression cluster:C4878

Full id: C4878_spleen_H9_HES3GFP_iPS_hippocampus_spinal_Neural

Phase1 CAGE Peaks

Hg19::chrX:69642952..69642968,+	p3@GDPD2
Hg19::chrX:69643029..69643035,+	p6@GDPD2
Hg19::chrX:69643047..69643060,+	p2@GDPD2

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
neuronal stem cell	2.39e-16	8
neural cell	6.12e-13	25
neuron	1.57e-12	6
neuroblast	1.57e-12	6
electrically signaling cell	1.57e-12	6
oligodendrocyte	5.41e-12	7
macroglial cell	5.41e-12	7
astrocyte	5.41e-12	7
oligodendrocyte precursor cell	5.41e-12	7
embryonic stem cell	8.68e-12	5
ectodermal cell	6.26e-08	71
neurectodermal cell	8.79e-08	59

Uber Anatomy

Ontology term	p-value	n
central nervous system	1.16e-88	82
neural tube	1.80e-87	57
neural rod	1.80e-87	57
future spinal cord	1.80e-87	57
neural keel	1.80e-87	57
regional part of nervous system	1.01e-76	94
nervous system	1.01e-76	94
regional part of brain	7.53e-74	59
neural plate	2.43e-69	86
presumptive neural plate	2.43e-69	86
brain	7.06e-68	69
future brain	7.06e-68	69
neurectoderm	1.72e-65	90
regional part of forebrain	1.30e-62	41
forebrain	1.30e-62	41
future forebrain	1.30e-62	41
anterior neural tube	7.31e-61	42
gray matter	1.28e-54	34
brain grey matter	1.28e-54	34
telencephalon	1.78e-54	34
regional part of telencephalon	7.49e-53	33
pre-chordal neural plate	1.72e-52	61
cerebral hemisphere	8.42e-51	32
ectoderm-derived structure	6.53e-46	169
head	9.18e-46	123
anterior region of body	1.89e-44	129
craniocervical region	1.89e-44	129
ectoderm	2.13e-44	173
presumptive ectoderm	2.13e-44	173
cerebral cortex	2.78e-38	25
pallium	2.78e-38	25
regional part of cerebral cortex	2.61e-33	22
adult organism	1.11e-32	115
neocortex	8.00e-30	20
posterior neural tube	1.50e-26	15
chordal neural plate	1.50e-26	15
segmental subdivision of hindbrain	1.65e-21	12
hindbrain	1.65e-21	12
presumptive hindbrain	1.65e-21	12
segmental subdivision of nervous system	1.30e-19	13
nucleus of brain	1.30e-17	9
neural nucleus	1.30e-17	9
basal ganglion	1.69e-17	9
nuclear complex of neuraxis	1.69e-17	9
aggregate regional part of brain	1.69e-17	9
collection of basal ganglia	1.69e-17	9
cerebral subcortex	1.69e-17	9
organ part	1.52e-16	219
tube	1.64e-16	194
regional part of metencephalon	8.01e-16	9
metencephalon	8.01e-16	9
future metencephalon	8.01e-16	9
telencephalic nucleus	6.09e-14	7
anatomical conduit	2.62e-12	241
brainstem	2.94e-12	8
temporal lobe	5.73e-12	7
anatomical cluster	1.01e-11	286
gyrus	1.65e-11	6
epithelium	3.37e-11	309
cell layer	6.21e-11	312
cerebellum	1.32e-10	6
rhombic lip	1.32e-10	6
limbic system	1.68e-10	5
parietal lobe	8.61e-10	5
organism subdivision	1.15e-09	365
diencephalon	1.97e-09	7
future diencephalon	1.97e-09	7
embryo	3.66e-09	612
corpus striatum	1.21e-08	4
striatum	1.21e-08	4
ventral part of telencephalon	1.21e-08	4
future corpus striatum	1.21e-08	4
organ	1.88e-07	511
medulla oblongata	2.19e-07	3
myelencephalon	2.19e-07	3
future myelencephalon	2.19e-07	3
multi-cellular organism	2.39e-07	659
brainstem nucleus	6.48e-07	3
pons	6.75e-07	3
caudate-putamen	7.61e-07	3
dorsal striatum	7.61e-07	3
middle temporal gyrus	9.46e-07	3

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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.028186023770617
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00669893875668565
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00311252330807245
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0110335515028583

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.