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Coexpression cluster:C561

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Full id: C561_brain_Neural_spinal_Neurons_parietal_temporal_occipital



Phase1 CAGE Peaks

Hg19::chr11:65816664..65816675,-p2@GAL3ST3
Hg19::chr13:36705425..36705445,-p5@DCLK1
Hg19::chr13:53422767..53422780,-p1@PCDH8
Hg19::chr19:19322758..19322773,+p1@NCAN
Hg19::chr19:19322805..19322812,+p2@NCAN
Hg19::chr1:156391550..156391569,-p2@C1orf61
Hg19::chr1:156399211..156399225,-p1@C1orf61
Hg19::chr1:156400037..156400063,-p@chr1:156400037..156400063
-
Hg19::chr22:42372970..42372971,+p5@SEPT3
Hg19::chr2:26395939..26396015,+p2@FAM59B
Hg19::chr3:26664252..26664268,+p5@LRRC3B
Hg19::chr3:65387362..65387385,-p14@MAGI1
Hg19::chr4:150999554..150999573,+p6@DCLK2
Hg19::chr5:140787600..140787637,+p2@PCDHGB6
Hg19::chr5:87968909..87968913,-p2@LINC00461
Hg19::chr5:87969130..87969153,-p1@LINC00461


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 IDGO nameFDR corrected p-value
GO:0022610biological adhesion0.00364590195774595
GO:0007155cell adhesion0.00364590195774595
GO:0016337cell-cell adhesion0.00364590195774595
GO:0050698proteoglycan sulfotransferase activity0.0170795551236903
GO:0030309poly-N-acetyllactosamine metabolic process0.0170795551236903
GO:0050694galactose 3-O-sulfotransferase activity0.0170795551236903
GO:0001733galactosylceramide sulfotransferase activity0.0170795551236903
GO:0017076purine nucleotide binding0.0170795551236903
GO:0007156homophilic cell adhesion0.0170795551236903
GO:00506563'-phosphoadenosine 5'-phosphosulfate binding0.0170795551236903
GO:0007158neuron adhesion0.0217324972662446
GO:0000166nucleotide binding0.0271439940753673
GO:0030554adenyl nucleotide binding0.0468748694812944
GO:0030166proteoglycan biosynthetic process0.0468748694812944
GO:0005509calcium ion binding0.0468748694812944
GO:0009311oligosaccharide metabolic process0.0468748694812944



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 termp-valuen
neuronal stem cell1.58e-158
neural cell1.02e-1225
neuron1.80e-116
neuroblast1.80e-116
electrically signaling cell1.80e-116
neurectodermal cell3.70e-0759
oligodendrocyte9.30e-077
macroglial cell9.30e-077
astrocyte9.30e-077
oligodendrocyte precursor cell9.30e-077
Uber Anatomy
Ontology termp-valuen
central nervous system3.98e-9681
nervous system1.86e-9589
neural tube2.70e-8956
neural rod2.70e-8956
future spinal cord2.70e-8956
neural keel2.70e-8956
regional part of nervous system1.13e-8353
regional part of brain1.13e-8353
brain1.28e-7268
future brain1.28e-7268
regional part of forebrain1.20e-6641
forebrain1.20e-6641
anterior neural tube1.20e-6641
future forebrain1.20e-6641
neurectoderm2.08e-6686
neural plate3.56e-6382
presumptive neural plate3.56e-6382
telencephalon3.07e-6234
brain grey matter5.98e-6234
gray matter5.98e-6234
cerebral hemisphere7.80e-5932
regional part of telencephalon1.84e-5832
ectoderm-derived structure1.50e-49171
ectoderm1.50e-49171
presumptive ectoderm1.50e-49171
ecto-epithelium3.88e-48104
pre-chordal neural plate5.32e-4861
adult organism3.31e-46114
cerebral cortex7.61e-4625
pallium7.61e-4625
regional part of cerebral cortex1.01e-4022
organ system subdivision8.07e-38223
structure with developmental contribution from neural crest2.42e-37132
neocortex9.28e-3720
posterior neural tube1.55e-2215
chordal neural plate1.55e-2215
segmental subdivision of nervous system7.12e-1913
anatomical cluster3.23e-18373
basal ganglion1.76e-179
nuclear complex of neuraxis1.76e-179
aggregate regional part of brain1.76e-179
collection of basal ganglia1.76e-179
cerebral subcortex1.76e-179
segmental subdivision of hindbrain2.10e-1712
hindbrain2.10e-1712
presumptive hindbrain2.10e-1712
neural nucleus3.62e-179
nucleus of brain3.62e-179
tube1.42e-16192
telencephalic nucleus7.61e-147
regional part of metencephalon1.14e-129
metencephalon1.14e-129
future metencephalon1.14e-129
gyrus1.29e-126
anatomical conduit1.57e-11240
brainstem2.25e-116
limbic system3.22e-115
parietal lobe4.94e-115
temporal lobe6.09e-116
occipital lobe8.00e-115
organ part1.69e-10218
embryo2.63e-10592
corpus striatum4.81e-094
striatum4.81e-094
ventral part of telencephalon4.81e-094
future corpus striatum4.81e-094
developing anatomical structure2.84e-08581
embryonic structure2.96e-08564
germ layer5.62e-08560
germ layer / neural crest5.62e-08560
embryonic tissue5.62e-08560
presumptive structure5.62e-08560
germ layer / neural crest derived structure5.62e-08560
epiblast (generic)5.62e-08560
regional part of diencephalon7.09e-084
cerebellum7.14e-086
rhombic lip7.14e-086
multi-tissue structure1.11e-07342
epithelium1.71e-07306
cell layer2.75e-07309
frontal cortex4.59e-073
caudate-putamen4.78e-073
dorsal striatum4.78e-073
multi-cellular organism6.51e-07656
spinal cord7.70e-073
dorsal region element7.70e-073
dorsum7.70e-073
diencephalon9.79e-077
future diencephalon9.79e-077


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#promotersEnrichmentp-valueq-value
SUZ12#2351239.39670892082430.003659155081411430.0184760441668695



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.