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Coexpression cluster:C4460

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Full id: C4460_brain_occipital_diencephalon_temporal_postcentral_olfactory_amygdala



Phase1 CAGE Peaks

  Short description
Hg19::chr5:132113042..132113061,- p4@SEPT8
Hg19::chr5:132113063..132113082,- p3@SEPT8
Hg19::chr5:132113083..132113109,- p2@SEPT8


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


No GOStat results

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


uberon_data


Uber Anatomy
Ontology termp-valuen
nervous system4.32e-3589
neural plate1.47e-3382
presumptive neural plate1.47e-3382
neurectoderm2.63e-3386
central nervous system1.71e-3281
neural tube2.22e-3156
neural rod2.22e-3156
future spinal cord2.22e-3156
neural keel2.22e-3156
ectoderm-derived structure4.85e-31171
ectoderm4.85e-31171
presumptive ectoderm4.85e-31171
brain7.14e-3168
future brain7.14e-3168
regional part of nervous system1.51e-2953
regional part of brain1.51e-2953
structure with developmental contribution from neural crest3.32e-28132
anatomical cluster9.72e-28373
ecto-epithelium5.38e-27104
pre-chordal neural plate6.25e-2761
cell layer3.97e-25309
epithelium9.31e-25306
regional part of forebrain1.42e-2341
forebrain1.42e-2341
anterior neural tube1.42e-2341
future forebrain1.42e-2341
organ part6.81e-22218
telencephalon3.43e-2134
brain grey matter3.56e-2134
gray matter3.56e-2134
tube3.17e-20192
cerebral hemisphere5.43e-2032
regional part of telencephalon6.36e-2032
multi-tissue structure3.08e-19342
anatomical conduit9.66e-18240
organ system subdivision6.02e-17223
adult organism2.07e-16114
cerebral cortex1.39e-1525
pallium1.39e-1525
regional part of cerebral cortex1.98e-1422
neocortex2.99e-1320
multi-cellular organism1.31e-11656
anatomical group6.00e-10625
anatomical system6.03e-10624
embryo1.32e-09592
posterior neural tube6.77e-0915
chordal neural plate6.77e-0915
developing anatomical structure2.76e-08581
segmental subdivision of nervous system9.75e-0813
segmental subdivision of hindbrain3.41e-0712
hindbrain3.41e-0712
presumptive hindbrain3.41e-0712
basal ganglion4.48e-079
nuclear complex of neuraxis4.48e-079
aggregate regional part of brain4.48e-079
collection of basal ganglia4.48e-079
cerebral subcortex4.48e-079
neural nucleus4.61e-079
nucleus of brain4.61e-079
germ layer7.39e-07560
germ layer / neural crest7.39e-07560
embryonic tissue7.39e-07560
presumptive structure7.39e-07560
germ layer / neural crest derived structure7.39e-07560
epiblast (generic)7.39e-07560
organ8.38e-07503


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)
MA0003.13.8806
MA0004.10.826076
MA0006.11.5435
MA0007.11.88666
MA0009.11.3275
MA0014.12.44638
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
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
MA0073.10.0185922
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
MA0101.10.646932
MA0103.10.628063
MA0105.11.5295
MA0106.10.986396
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
MA0144.12.26598
MA0145.10.273764
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.23.92311
MA0104.21.2307
MA0047.20.973066
MA0112.21.34467
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.12.30945
MA0155.12.02721
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.54885
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


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

TF#promotersEnrichmentp-valueq-value
E2F1#186934.907389214879320.008460985347239390.0327050167911594
E2F6#187635.017155731697390.00791769806886330.0323798444911118
ELF1#199734.258097958807540.01295179875054610.0464325453009846
GABPB1#255337.067683836182170.002832212825417420.0154647082801156
NFKB1#479035.488063424193840.006049381815655430.027051654354324
PAX5#507936.669565531177830.003370290999677260.0173488009125779
SIX5#147912317.0867153554590.0002004060546325010.00240190589164147
YY1#752834.911170749853860.008441455341808260.0330775955593409
ZBTB7A#5134137.35190930787590.002516255860282270.014071281098309
ZNF143#7702313.50087655222790.0004062804962997170.00390246746556112



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.