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Coexpression cluster:C989

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Full id: C989_optic_globus_medial_thalamus_spinal_occipital_parietal



Phase1 CAGE Peaks

  Short description
Hg19::chr11:117304153..117304157,- p@chr11:117304153..117304157
-
Hg19::chr11:40315134..40315154,- p10@LRRC4C
Hg19::chr12:123319279..123319305,+ p2@HIP1R
Hg19::chr13:78320835..78320853,+ p@chr13:78320835..78320853
+
Hg19::chr16:1031491..1031496,- p7@LMF1
Hg19::chr20:58179554..58179578,+ p2@PHACTR3
Hg19::chr20:58179582..58179601,+ p1@PHACTR3
Hg19::chr8:3014504..3014509,- p@chr8:3014504..3014509
-


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0003779actin binding0.0326377961348001
GO:0008092cytoskeletal protein binding0.0326377961348001
GO:0050770regulation of axonogenesis0.0362675180022866
GO:0004864protein phosphatase inhibitor activity0.0362675180022866
GO:0019212phosphatase inhibitor activity0.0362675180022866
GO:0050767regulation of neurogenesis0.0362675180022866
GO:0005905coated pit0.0362675180022866
GO:0016363nuclear matrix0.0362675180022866



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
neuronal stem cell3.75e-078
Uber Anatomy
Ontology termp-valuen
neural tube4.95e-10056
neural rod4.95e-10056
future spinal cord4.95e-10056
neural keel4.95e-10056
nervous system4.04e-9389
regional part of nervous system4.33e-9353
regional part of brain4.33e-9353
central nervous system1.33e-9181
regional part of forebrain5.02e-8041
forebrain5.02e-8041
anterior neural tube5.02e-8041
future forebrain5.02e-8041
brain4.29e-7568
future brain4.29e-7568
neural plate7.20e-7082
presumptive neural plate7.20e-7082
neurectoderm1.33e-6886
brain grey matter1.63e-6534
gray matter1.63e-6534
telencephalon2.58e-6534
regional part of telencephalon4.38e-6132
cerebral hemisphere6.35e-6132
pre-chordal neural plate2.75e-5661
adult organism2.93e-56114
ecto-epithelium4.55e-54104
regional part of cerebral cortex1.25e-4722
ectoderm-derived structure8.90e-46171
ectoderm8.90e-46171
presumptive ectoderm8.90e-46171
cerebral cortex5.49e-4525
pallium5.49e-4525
neocortex4.30e-4320
structure with developmental contribution from neural crest5.22e-43132
organ system subdivision2.69e-40223
tube2.82e-22192
basal ganglion2.91e-229
nuclear complex of neuraxis2.91e-229
aggregate regional part of brain2.91e-229
collection of basal ganglia2.91e-229
cerebral subcortex2.91e-229
neural nucleus8.41e-229
nucleus of brain8.41e-229
anatomical cluster6.50e-21373
posterior neural tube2.31e-2015
chordal neural plate2.31e-2015
telencephalic nucleus1.55e-177
segmental subdivision of nervous system1.68e-1613
diencephalon1.21e-157
future diencephalon1.21e-157
anatomical conduit5.63e-15240
gyrus1.02e-146
segmental subdivision of hindbrain2.53e-1412
hindbrain2.53e-1412
presumptive hindbrain2.53e-1412
brainstem1.22e-136
limbic system6.94e-135
temporal lobe1.00e-126
occipital lobe1.09e-125
parietal lobe2.13e-125
organ part2.25e-12218
multi-tissue structure4.56e-12342
epithelium2.54e-11306
cell layer4.50e-11309
corpus striatum1.12e-104
striatum1.12e-104
ventral part of telencephalon1.12e-104
future corpus striatum1.12e-104
regional part of diencephalon5.64e-104
embryo6.03e-10592
developing anatomical structure2.64e-09581
germ layer2.94e-09560
germ layer / neural crest2.94e-09560
embryonic tissue2.94e-09560
presumptive structure2.94e-09560
germ layer / neural crest derived structure2.94e-09560
epiblast (generic)2.94e-09560
embryonic structure4.67e-09564
regional part of metencephalon5.27e-099
metencephalon5.27e-099
future metencephalon5.27e-099
gland of diencephalon5.65e-094
neuroendocrine gland5.65e-094
caudate-putamen1.13e-083
dorsal striatum1.13e-083
frontal cortex2.65e-083
organ3.31e-08503
spinal cord3.63e-083
dorsal region element3.63e-083
dorsum3.63e-083
pons8.48e-083
medulla oblongata1.65e-073
myelencephalon1.65e-073
future myelencephalon1.65e-073
anatomical system2.49e-07624
anatomical group2.75e-07625
multi-cellular organism4.97e-07656


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.393486
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.11.38556
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.653157
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.835832
MA0056.10
MA0057.10.305162
MA0058.10.950944
MA0059.10.948176
MA0060.10.556724
MA0061.10.497495
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.823119
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.111.1158
MA0074.11.36092
MA0076.10.377799
MA0077.10.880402
MA0078.11.57046
MA0081.10.948525
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.11.6523
MA0089.10
MA0090.10.391903
MA0091.13.00258
MA0092.10.421159
MA0093.10.818737
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.11.47197
MA0106.10.59853
MA0107.10.666147
MA0108.20.753643
MA0109.10
MA0111.11.04489
MA0113.10.614917
MA0114.10.655057
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.11.49284
MA0144.10.218541
MA0145.10.0613434
MA0146.10.113833
MA0147.10.681318
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.22.17723
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.21.05746
MA0047.20.586412
MA0112.20.458158
MA0065.20.490252
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.274121
MA0155.10.43752
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.625961
MA0163.10.288263
MA0164.10.627336
MA0080.20.303167
MA0018.21.46097
MA0099.20.523145
MA0079.24.79691
MA0102.21.46209
MA0258.11.13653
MA0259.10.699589
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


No analysis results for this cluster

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.