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Coexpression cluster:C3827

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Full id: C3827_globus_locus_caudate_cerebral_parietal_thalamus_occipital



Phase1 CAGE Peaks

  Short description
Hg19::chr19:57322667..57322678,- p@chr19:57322667..57322678
-
Hg19::chr19:57324701..57324716,- p2@PEG3
Hg19::chr20:34818589..34818600,+ p@chr20:34818589..34818600
+


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
neural tube2.05e-8656
neural rod2.05e-8656
future spinal cord2.05e-8656
neural keel2.05e-8656
regional part of nervous system5.31e-7853
regional part of brain5.31e-7853
regional part of forebrain8.18e-6741
forebrain8.18e-6741
anterior neural tube8.18e-6741
future forebrain8.18e-6741
central nervous system1.05e-6581
brain9.14e-6568
future brain9.14e-6568
nervous system3.30e-6489
brain grey matter6.89e-6234
gray matter6.89e-6234
telencephalon6.81e-6134
neural plate3.79e-5982
presumptive neural plate3.79e-5982
neurectoderm7.41e-5986
cerebral hemisphere7.54e-5632
regional part of telencephalon8.11e-5632
adult organism4.31e-49114
ecto-epithelium6.19e-47104
pre-chordal neural plate1.20e-4561
regional part of cerebral cortex8.97e-4222
structure with developmental contribution from neural crest1.14e-36132
cerebral cortex2.19e-3625
pallium2.19e-3625
neocortex6.42e-3620
ectoderm-derived structure1.09e-31171
ectoderm1.09e-31171
presumptive ectoderm1.09e-31171
neural nucleus1.02e-289
nucleus of brain1.02e-289
organ system subdivision7.28e-28223
tube7.24e-23192
basal ganglion1.48e-229
nuclear complex of neuraxis1.48e-229
aggregate regional part of brain1.48e-229
collection of basal ganglia1.48e-229
cerebral subcortex1.48e-229
telencephalic nucleus2.21e-227
posterior neural tube8.90e-2015
chordal neural plate8.90e-2015
brainstem1.31e-196
gyrus3.22e-196
anatomical conduit4.34e-17240
parietal lobe4.51e-165
segmental subdivision of nervous system6.53e-1513
corpus striatum1.57e-134
striatum1.57e-134
ventral part of telencephalon1.57e-134
future corpus striatum1.57e-134
epithelium1.07e-12306
organ part1.52e-12218
cell layer1.84e-12309
segmental subdivision of hindbrain1.87e-1212
hindbrain1.87e-1212
presumptive hindbrain1.87e-1212
anatomical cluster7.71e-12373
caudate-putamen3.64e-113
dorsal striatum3.64e-113
pons7.52e-113
limbic system9.00e-115
occipital lobe1.42e-105
medulla oblongata1.75e-103
myelencephalon1.75e-103
future myelencephalon1.75e-103
spinal cord2.48e-103
dorsal region element2.48e-103
dorsum2.48e-103
multi-tissue structure2.21e-09342
regional part of diencephalon4.12e-084
caudate nucleus4.30e-082
future caudate nucleus4.30e-082
locus ceruleus4.76e-082
brainstem nucleus4.76e-082
hindbrain nucleus4.76e-082
globus pallidus5.82e-082
pallidum5.82e-082
Ammon's horn6.88e-082
lobe parts of cerebral cortex6.88e-082
hippocampal formation6.88e-082
limbic lobe6.88e-082
temporal lobe7.66e-086
embryonic structure7.83e-08564
middle temporal gyrus7.86e-082
dorsal plus ventral thalamus7.86e-082
middle frontal gyrus7.86e-082
thalamic complex7.86e-082
organ8.41e-08503
diencephalon8.83e-087
future diencephalon8.83e-087
germ layer2.31e-07560
germ layer / neural crest2.31e-07560
embryonic tissue2.31e-07560
presumptive structure2.31e-07560
germ layer / neural crest derived structure2.31e-07560
epiblast (generic)2.31e-07560


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0057.10.333427
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
MA0070.12.89432
MA0071.10.897953
MA0072.11.29561
MA0073.11.36698
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
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
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.09178
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.