Coexpression cluster:C1942

Full id: C1942_Neural_spinal_Astrocyte_Neurons_caudate_locus_medial

Phase1 CAGE Peaks

Hg19::chr4:57547751..57547764,-	p6@HOPX
Hg19::chr4:57547773..57547780,-	p12@HOPX
Hg19::chr4:57547820..57547829,-	p8@HOPX
Hg19::chr4:57547870..57547873,-	p11@HOPX
Hg19::chr6:111894900..111894919,-	p13@TRAF3IP2

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:0043416	regulation of skeletal muscle regeneration	0.00104792181796774
GO:0051153	regulation of striated muscle cell differentiation	0.00104792181796774
GO:0043415	positive regulation of skeletal muscle regeneration	0.00104792181796774
GO:0051149	positive regulation of muscle cell differentiation	0.00104792181796774
GO:0051155	positive regulation of striated muscle cell differentiation	0.00104792181796774
GO:0051147	regulation of muscle cell differentiation	0.0029939301333032
GO:0043403	skeletal muscle regeneration	0.0029939301333032
GO:0048522	positive regulation of cellular process	0.00785744710401431
GO:0051146	striated muscle cell differentiation	0.00785744710401431
GO:0042246	tissue regeneration	0.00785744710401431
GO:0048518	positive regulation of biological process	0.00785744710401431
GO:0031099	regeneration	0.00785744710401431
GO:0048589	developmental growth	0.0149048318470955
GO:0042692	muscle cell differentiation	0.0164063264175261
GO:0045597	positive regulation of cell differentiation	0.0164063264175261
GO:0051094	positive regulation of developmental process	0.0222463790385095
GO:0014706	striated muscle development	0.0270879516452688
GO:0007507	heart development	0.0272617417255358
GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB cascade	0.0272617417255358
GO:0043122	regulation of I-kappaB kinase/NF-kappaB cascade	0.0282493298120415
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.0311397934867029
GO:0042060	wound healing	0.0311397934867029
GO:0007249	I-kappaB kinase/NF-kappaB cascade	0.0313714865634195
GO:0045595	regulation of cell differentiation	0.0313714865634195
GO:0009967	positive regulation of signal transduction	0.0319946685882814
GO:0007517	muscle development	0.0345747901444914
GO:0045892	negative regulation of transcription, DNA-dependent	0.0392769744282824
GO:0016564	transcription repressor activity	0.0399200397743542
GO:0050793	regulation of developmental process	0.0424920942631532

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
astrocyte of the cerebral cortex	3.05e-10	3
acinar cell of salivary gland	1.68e-08	3

Uber Anatomy

Ontology term	p-value	n
neural tube	5.24e-100	56
neural rod	5.24e-100	56
future spinal cord	5.24e-100	56
neural keel	5.24e-100	56
central nervous system	1.76e-93	81
regional part of nervous system	3.82e-91	53
regional part of brain	3.82e-91	53
nervous system	5.10e-83	89
brain grey matter	2.97e-79	34
gray matter	2.97e-79	34
telencephalon	3.58e-79	34
regional part of forebrain	1.42e-77	41
forebrain	1.42e-77	41
anterior neural tube	1.42e-77	41
future forebrain	1.42e-77	41
brain	5.85e-75	68
future brain	5.85e-75	68
cerebral hemisphere	3.68e-74	32
regional part of telencephalon	1.13e-73	32
neural plate	8.67e-68	82
presumptive neural plate	8.67e-68	82
neurectoderm	4.20e-64	86
cerebral cortex	6.91e-56	25
pallium	6.91e-56	25
pre-chordal neural plate	2.68e-52	61
adult organism	4.49e-52	114
ecto-epithelium	5.36e-51	104
regional part of cerebral cortex	2.30e-47	22
ectoderm-derived structure	2.30e-44	171
ectoderm	2.30e-44	171
presumptive ectoderm	2.30e-44	171
structure with developmental contribution from neural crest	1.48e-43	132
neocortex	7.74e-42	20
organ system subdivision	4.75e-35	223
neural nucleus	2.49e-24	9
nucleus of brain	2.49e-24	9
basal ganglion	3.12e-24	9
nuclear complex of neuraxis	3.12e-24	9
aggregate regional part of brain	3.12e-24	9
collection of basal ganglia	3.12e-24	9
cerebral subcortex	3.12e-24	9
tube	2.00e-23	192
posterior neural tube	2.19e-22	15
chordal neural plate	2.19e-22	15
anatomical conduit	2.61e-19	240
telencephalic nucleus	6.07e-19	7
anatomical cluster	5.06e-18	373
gyrus	6.13e-18	6
brainstem	1.10e-17	6
limbic system	4.01e-15	5
temporal lobe	7.95e-15	6
segmental subdivision of hindbrain	1.20e-14	12
hindbrain	1.20e-14	12
presumptive hindbrain	1.20e-14	12
segmental subdivision of nervous system	2.09e-13	13
organ part	5.87e-13	218
epithelium	1.60e-12	306
cell layer	2.77e-12	309
corpus striatum	5.44e-12	4
striatum	5.44e-12	4
ventral part of telencephalon	5.44e-12	4
future corpus striatum	5.44e-12	4
multi-tissue structure	5.23e-11	342
spinal cord	1.70e-10	3
dorsal region element	1.70e-10	3
dorsum	1.70e-10	3
parietal lobe	6.35e-10	5
frontal cortex	7.07e-10	3
occipital lobe	8.37e-10	5
medulla oblongata	8.71e-10	3
myelencephalon	8.71e-10	3
future myelencephalon	8.71e-10	3
pons	1.31e-09	3
caudate-putamen	1.92e-09	3
dorsal striatum	1.92e-09	3
germ layer	7.08e-09	560
germ layer / neural crest	7.08e-09	560
embryonic tissue	7.08e-09	560
presumptive structure	7.08e-09	560
germ layer / neural crest derived structure	7.08e-09	560
epiblast (generic)	7.08e-09	560
embryonic structure	1.04e-08	564
organ	1.11e-08	503
embryo	3.48e-08	592
developing anatomical structure	5.14e-08	581
regional part of metencephalon	5.70e-08	9
metencephalon	5.70e-08	9
future metencephalon	5.70e-08	9
Ammon's horn	2.87e-07	2
lobe parts of cerebral cortex	2.87e-07	2
hippocampal formation	2.87e-07	2
limbic lobe	2.87e-07	2
locus ceruleus	4.38e-07	2
brainstem nucleus	4.38e-07	2
hindbrain nucleus	4.38e-07	2
middle temporal gyrus	4.94e-07	2
caudate nucleus	5.09e-07	2
future caudate nucleus	5.09e-07	2

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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
SPI1#6688	4	6.56345880681818	0.000995742963645402	0.00714394445147779
STAT3#6774	4	8.41557199772339	0.000377152721159863	0.00374424458604705

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.