Coexpression cluster:C3149

Full id: C3149_occipital_diencephalon_olfactory_cerebral_amygdala_caudate_hippocampus

Phase1 CAGE Peaks

Hg19::chr11:35280532..35280559,-	p11@SLC1A2
Hg19::chr12:57978901..57978913,+	p3@uc001sos.2
Hg19::chr3:58551927..58551941,-	p@chr3:58551927..58551941 -

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:0005313	L-glutamate transmembrane transporter activity	0.00321693495483676
GO:0015172	acidic amino acid transmembrane transporter activity	0.00321693495483676
GO:0015813	L-glutamate transport	0.00321693495483676
GO:0015800	acidic amino acid transport	0.00321693495483676
GO:0017153	sodium:dicarboxylate symporter activity	0.00321693495483676
GO:0005310	dicarboxylic acid transmembrane transporter activity	0.00321693495483676
GO:0006835	dicarboxylic acid transport	0.00321693495483676
GO:0015179	L-amino acid transmembrane transporter activity	0.00516601907453197
GO:0005343	organic acid:sodium symporter activity	0.00516601907453197
GO:0015296	anion:cation symporter activity	0.00516601907453197
GO:0015171	amino acid transmembrane transporter activity	0.00728541151536559
GO:0006865	amino acid transport	0.00728541151536559
GO:0015837	amine transport	0.00728541151536559
GO:0015370	solute:sodium symporter activity	0.00728541151536559
GO:0046943	carboxylic acid transmembrane transporter activity	0.00728541151536559
GO:0046942	carboxylic acid transport	0.00728541151536559
GO:0005342	organic acid transmembrane transporter activity	0.00728541151536559
GO:0015849	organic acid transport	0.00728541151536559
GO:0015294	solute:cation symporter activity	0.0079477216531261
GO:0008509	anion transmembrane transporter activity	0.0138422818791946
GO:0015293	symporter activity	0.0152646717464803
GO:0007268	synaptic transmission	0.0174609036318679
GO:0019226	transmission of nerve impulse	0.019005421344432
GO:0015291	secondary active transmembrane transporter activity	0.0198693041328153
GO:0007267	cell-cell signaling	0.0335079869696613
GO:0022804	active transmembrane transporter activity	0.0335079869696613
GO:0005624	membrane fraction	0.0335079869696613
GO:0008324	cation transmembrane transporter activity	0.0412002582248261
GO:0000267	cell fraction	0.0412002582248261

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>

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Uber Anatomy

Ontology term	p-value	n
adult organism	2.24e-76	115
neural tube	2.20e-64	57
neural rod	2.20e-64	57
future spinal cord	2.20e-64	57
neural keel	2.20e-64	57
central nervous system	5.95e-60	82
regional part of nervous system	4.50e-56	94
nervous system	4.50e-56	94
regional part of brain	1.93e-53	59
regional part of forebrain	1.36e-51	41
forebrain	1.36e-51	41
future forebrain	1.36e-51	41
brain	9.84e-51	69
future brain	9.84e-51	69
neural plate	2.48e-50	86
presumptive neural plate	2.48e-50	86
anterior neural tube	4.93e-50	42
neurectoderm	7.41e-49	90
gray matter	4.16e-43	34
brain grey matter	4.16e-43	34
telencephalon	5.50e-43	34
regional part of telencephalon	1.28e-41	33
cerebral hemisphere	1.94e-40	32
pre-chordal neural plate	2.92e-33	61
cerebral cortex	1.59e-30	25
pallium	1.59e-30	25
regional part of cerebral cortex	2.58e-30	22
ectoderm-derived structure	1.67e-29	169
ectoderm	2.85e-29	173
presumptive ectoderm	2.85e-29	173
neocortex	2.35e-27	20
head	2.93e-27	123
anterior region of body	4.22e-27	129
craniocervical region	4.22e-27	129
tube	2.55e-20	194
anatomical conduit	9.29e-20	241
anatomical cluster	3.67e-17	286
posterior neural tube	6.40e-15	15
chordal neural plate	6.40e-15	15
basal ganglion	3.05e-14	9
nuclear complex of neuraxis	3.05e-14	9
aggregate regional part of brain	3.05e-14	9
collection of basal ganglia	3.05e-14	9
cerebral subcortex	3.05e-14	9
nucleus of brain	6.16e-14	9
neural nucleus	6.16e-14	9
segmental subdivision of nervous system	2.70e-12	13
telencephalic nucleus	2.87e-11	7
epithelium	4.40e-11	309
segmental subdivision of hindbrain	5.29e-11	12
hindbrain	5.29e-11	12
presumptive hindbrain	5.29e-11	12
cell layer	9.12e-11	312
organ part	5.32e-10	219
gyrus	5.49e-10	6
diencephalon	8.14e-10	7
future diencephalon	8.14e-10	7
temporal lobe	8.26e-10	7
multi-tissue structure	2.85e-09	347
brainstem	4.89e-09	8
limbic system	7.66e-09	5
embryo	9.14e-09	612
occipital lobe	1.35e-08	5
parietal lobe	3.19e-08	5
organ	5.40e-08	511
embryonic structure	5.41e-08	605
developing anatomical structure	5.41e-08	605
multi-cellular organism	6.73e-08	659
germ layer	1.25e-07	604
embryonic tissue	1.25e-07	604
presumptive structure	1.25e-07	604
epiblast (generic)	1.25e-07	604
organism subdivision	1.35e-07	365
regional part of metencephalon	2.28e-07	9
metencephalon	2.28e-07	9
future metencephalon	2.28e-07	9
corpus striatum	3.33e-07	4
striatum	3.33e-07	4
ventral part of telencephalon	3.33e-07	4
future corpus striatum	3.33e-07	4
anatomical system	8.27e-07	625
anatomical group	9.52e-07	626

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.