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Coexpression cluster:C3878

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Full id: C3878_retina_temporal_amygdala_nucleus_putamen_insula_olfactory



Phase1 CAGE Peaks

  Short description
Hg19::chr1:156117128..156117137,+ p11@SEMA4A
Hg19::chr1:156117149..156117176,+ p3@SEMA4A
Hg19::chr21:45725050..45725074,+ p2@PFKL


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:0006002fructose 6-phosphate metabolic process0.00871267308455652
GO:0006110regulation of glycolysis0.00871267308455652
GO:00059456-phosphofructokinase complex0.0174191905249608
GO:00038726-phosphofructokinase activity0.0174191905249608
GO:0006000fructose metabolic process0.0174191905249608
GO:0009894regulation of catabolic process0.0174191905249608
GO:0008443phosphofructokinase activity0.0174191905249608
GO:0019200carbohydrate kinase activity0.0321019727997267
GO:0006096glycolysis0.0490648290538933
GO:0006007glucose catabolic process0.0490648290538933
GO:0019320hexose catabolic process0.0490648290538933
GO:0046365monosaccharide catabolic process0.0490648290538933
GO:0046164alcohol catabolic process0.0490648290538933
GO:0044275cellular carbohydrate catabolic process0.0490648290538933
GO:0044445cytosolic part0.0490648290538933
GO:0016052carbohydrate catabolic process0.0490648290538933
GO:0006006glucose metabolic process0.0490648290538933



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
retinal pigment epithelial cell2.22e-093
visual pigment cell3.94e-074
Uber Anatomy
Ontology termp-valuen
neural tube4.59e-9056
neural rod4.59e-9056
future spinal cord4.59e-9056
neural keel4.59e-9056
regional part of nervous system4.80e-8253
regional part of brain4.80e-8253
central nervous system2.54e-7481
neural plate3.62e-7482
presumptive neural plate3.62e-7482
brain3.08e-7168
future brain3.08e-7168
neurectoderm3.44e-7086
nervous system1.01e-6889
regional part of forebrain2.53e-6841
forebrain2.53e-6841
anterior neural tube2.53e-6841
future forebrain2.53e-6841
telencephalon2.60e-6834
brain grey matter1.15e-6734
gray matter1.15e-6734
cerebral hemisphere8.61e-6332
regional part of telencephalon1.77e-6232
pre-chordal neural plate2.83e-5961
ecto-epithelium4.85e-56104
adult organism3.12e-53114
regional part of cerebral cortex2.65e-5022
structure with developmental contribution from neural crest6.13e-48132
neocortex8.01e-4520
cerebral cortex7.77e-4425
pallium7.77e-4425
ectoderm-derived structure8.16e-39171
ectoderm8.16e-39171
presumptive ectoderm8.16e-39171
basal ganglion3.84e-269
nuclear complex of neuraxis3.84e-269
aggregate regional part of brain3.84e-269
collection of basal ganglia3.84e-269
cerebral subcortex3.84e-269
neural nucleus1.26e-259
nucleus of brain1.26e-259
organ system subdivision4.71e-24223
posterior neural tube1.06e-2115
chordal neural plate1.06e-2115
tube6.85e-21192
telencephalic nucleus1.53e-207
gyrus2.53e-196
brainstem1.37e-176
anatomical cluster2.19e-16373
temporal lobe5.99e-166
limbic system1.20e-155
segmental subdivision of hindbrain1.53e-1412
hindbrain1.53e-1412
presumptive hindbrain1.53e-1412
anatomical conduit1.74e-14240
organ part5.34e-14218
epithelium1.59e-13306
segmental subdivision of nervous system2.57e-1313
cell layer2.82e-13309
corpus striatum8.80e-134
striatum8.80e-134
ventral part of telencephalon8.80e-134
future corpus striatum8.80e-134
multi-tissue structure9.82e-11342
parietal lobe1.54e-105
occipital lobe2.27e-105
frontal cortex2.79e-103
caudate-putamen6.56e-103
dorsal striatum6.56e-103
medulla oblongata8.10e-103
myelencephalon8.10e-103
future myelencephalon8.10e-103
organ8.71e-10503
spinal cord1.13e-093
dorsal region element1.13e-093
dorsum1.13e-093
pons1.76e-093
pigmented layer of retina2.22e-093
presumptive retinal pigmented epithelium2.22e-093
retina2.59e-086
photoreceptor array2.59e-086
posterior segment of eyeball2.59e-086
regional part of metencephalon7.18e-089
metencephalon7.18e-089
future metencephalon7.18e-089
middle temporal gyrus1.23e-072
middle frontal gyrus2.03e-072
embryo2.58e-07592
amygdala2.69e-072
caudate nucleus2.77e-072
future caudate nucleus2.77e-072
Ammon's horn3.77e-072
lobe parts of cerebral cortex3.77e-072
hippocampal formation3.77e-072
limbic lobe3.77e-072
developing anatomical structure3.88e-07581
layer of retina3.94e-074
dorsal plus ventral thalamus4.39e-072
thalamic complex4.39e-072


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.211629
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.12.03569
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.11.55947
MA0103.11.52002
MA0105.10.31555
MA0106.12.25834
MA0107.11.36919
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.11.37817
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.15986
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.21.34467
MA0065.22.13692
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.12.83144
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.941469
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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.