Coexpression cluster:C1198

Full id: C1198_Neural_parietal_occipital_Astrocyte_brain_duodenum_temporal

Phase1 CAGE Peaks

Hg19::chr14:29234581..29234601,+	p2@FOXG1
Hg19::chr3:13083919..13083940,-	p@chr3:13083919..13083940 -
Hg19::chr3:26664291..26664329,+	p1@LRRC3B
Hg19::chr6:118228389..118228435,+	p1@SLC35F1
Hg19::chr8:28351707..28351781,+	p1@FZD3
Hg19::chr9:126774018..126774055,+	p1@LHX2
Hg19::chr9:126774058..126774081,+	p3@LHX2

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

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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

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GO ID	GO name	FDR corrected p-value
GO:0007399	nervous system development	0.00857355975151682
GO:0007420	brain development	0.00857355975151682
GO:0048513	organ development	0.012219673955238
GO:0007417	central nervous system development	0.012219673955238
GO:0001736	establishment of planar polarity	0.0133886523705115
GO:0001738	morphogenesis of a polarized epithelium	0.0133886523705115
GO:0048731	system development	0.0133886523705115
GO:0007164	establishment of tissue polarity	0.0133886523705115
GO:0042813	Wnt receptor activity	0.013600369910269
GO:0001843	neural tube closure	0.0152905103453416
GO:0014020	primary neural tube formation	0.0152905103453416
GO:0048856	anatomical structure development	0.0152905103453416
GO:0004926	non-G-protein coupled 7TM receptor activity	0.0152905103453416
GO:0001839	neural plate morphogenesis	0.0152905103453416
GO:0001841	neural tube formation	0.0152905103453416
GO:0001840	neural plate development	0.0152905103453416
GO:0001838	embryonic epithelial tube formation	0.0152905103453416
GO:0007275	multicellular organismal development	0.0152905103453416
GO:0021915	neural tube development	0.0152905103453416
GO:0016331	morphogenesis of embryonic epithelium	0.0168165908635914
GO:0042472	inner ear morphogenesis	0.0194503404689869
GO:0009953	dorsal/ventral pattern formation	0.0194503404689869
GO:0042471	ear morphogenesis	0.0205943935320225
GO:0048839	inner ear development	0.0241829077621319
GO:0043583	ear development	0.0248812194198963
GO:0043565	sequence-specific DNA binding	0.0248812194198963
GO:0007498	mesoderm development	0.0248812194198963
GO:0032502	developmental process	0.0304572556182887
GO:0002009	morphogenesis of an epithelium	0.0331313768523156
GO:0032501	multicellular organismal process	0.038969389921935
GO:0035239	tube morphogenesis	0.038969389921935
GO:0045177	apical part of cell	0.038969389921935
GO:0007423	sensory organ development	0.038969389921935
GO:0003002	regionalization	0.038969389921935
GO:0048598	embryonic morphogenesis	0.0390841434722103
GO:0009792	embryonic development ending in birth or egg hatching	0.0390841434722103
GO:0043009	chordate embryonic development	0.0390841434722103
GO:0035295	tube development	0.0468078249567275
GO:0003700	transcription factor activity	0.0471084598502684
GO:0007389	pattern specification process	0.0471084598502684

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>

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Cell Type

Ontology term	p-value	n
neural cell	1.81e-09	25
embryonic stem cell	9.40e-08	5
astrocyte of the cerebral cortex	7.23e-07	3
neurectodermal cell	9.23e-07	59

Uber Anatomy

Ontology term	p-value	n
central nervous system	6.52e-68	81
neural tube	6.51e-66	56
neural rod	6.51e-66	56
future spinal cord	6.51e-66	56
neural keel	6.51e-66	56
nervous system	1.23e-65	89
regional part of nervous system	7.24e-65	53
regional part of brain	7.24e-65	53
neural plate	5.38e-61	82
presumptive neural plate	5.38e-61	82
brain	1.77e-58	68
future brain	1.77e-58	68
neurectoderm	2.81e-57	86
regional part of forebrain	4.19e-55	41
forebrain	4.19e-55	41
anterior neural tube	4.19e-55	41
future forebrain	4.19e-55	41
telencephalon	1.74e-54	34
brain grey matter	5.94e-54	34
gray matter	5.94e-54	34
pre-chordal neural plate	4.69e-53	61
cerebral hemisphere	9.92e-52	32
regional part of telencephalon	2.45e-51	32
ecto-epithelium	1.44e-47	104
ectoderm-derived structure	7.22e-41	171
ectoderm	7.22e-41	171
presumptive ectoderm	7.22e-41	171
cerebral cortex	1.53e-40	25
pallium	1.53e-40	25
structure with developmental contribution from neural crest	3.23e-40	132
regional part of cerebral cortex	3.00e-35	22
neocortex	6.91e-32	20
adult organism	2.10e-28	114
organ system subdivision	2.37e-26	223
anatomical cluster	2.72e-18	373
basal ganglion	2.26e-15	9
nuclear complex of neuraxis	2.26e-15	9
aggregate regional part of brain	2.26e-15	9
collection of basal ganglia	2.26e-15	9
cerebral subcortex	2.26e-15	9
organ part	1.13e-14	218
neural nucleus	1.42e-14	9
nucleus of brain	1.42e-14	9
tube	6.23e-13	192
posterior neural tube	3.58e-12	15
chordal neural plate	3.58e-12	15
telencephalic nucleus	4.36e-12	7
gyrus	3.06e-11	6
epithelium	3.92e-11	306
segmental subdivision of hindbrain	5.46e-11	12
hindbrain	5.46e-11	12
presumptive hindbrain	5.46e-11	12
cell layer	7.65e-11	309
segmental subdivision of nervous system	5.67e-10	13
multi-tissue structure	6.22e-10	342
limbic system	7.15e-10	5
regional part of metencephalon	7.97e-10	9
metencephalon	7.97e-10	9
future metencephalon	7.97e-10	9
temporal lobe	1.00e-09	6
occipital lobe	1.19e-09	5
embryo	1.71e-09	592
parietal lobe	2.08e-09	5
pigment epithelium of eye	1.58e-08	11
anatomical conduit	2.06e-08	240
corpus striatum	4.37e-08	4
striatum	4.37e-08	4
ventral part of telencephalon	4.37e-08	4
future corpus striatum	4.37e-08	4
multi-cellular organism	3.91e-07	656
organ	7.27e-07	503
developing anatomical structure	7.88e-07	581
atypical epithelium	8.20e-07	4

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

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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

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No analysis results for this cluster

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

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This analysis result is provided for C0 - C305 clusters.