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Coexpression cluster:C3945

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Full id: C3945_retina_medulla_substantia_thalamus_spinal_locus_globus



Phase1 CAGE Peaks

  Short description
Hg19::chr1:226923935..226923978,- p4@ITPKB
Hg19::chr4:170948331..170948352,- p6@MFAP3L
Hg19::chr4:170948418..170948434,- p7@MFAP3L


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:0008440inositol trisphosphate 3-kinase activity0.00947658037871165
GO:0051766inositol trisphosphate kinase activity0.00947658037871165
GO:0004428inositol or phosphatidylinositol kinase activity0.0297607388808228
GO:0005516calmodulin binding0.0476321313956351



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 tube1.33e-6456
neural rod1.33e-6456
future spinal cord1.33e-6456
neural keel1.33e-6456
regional part of nervous system3.79e-6253
regional part of brain3.79e-6253
adult organism4.10e-60114
brain3.63e-5468
future brain3.63e-5468
regional part of forebrain8.48e-5441
forebrain8.48e-5441
anterior neural tube8.48e-5441
future forebrain8.48e-5441
central nervous system2.80e-5081
nervous system8.02e-5089
brain grey matter1.35e-4834
gray matter1.35e-4834
telencephalon2.60e-4834
neural plate5.93e-4882
presumptive neural plate5.93e-4882
neurectoderm6.70e-4786
regional part of telencephalon8.92e-4532
cerebral hemisphere1.20e-4432
pre-chordal neural plate2.63e-4161
ecto-epithelium3.91e-36104
cerebral cortex3.18e-3225
pallium3.18e-3225
regional part of cerebral cortex6.34e-3122
neocortex1.76e-2720
structure with developmental contribution from neural crest2.38e-26132
ectoderm-derived structure1.59e-23171
ectoderm1.59e-23171
presumptive ectoderm1.59e-23171
neural nucleus4.94e-189
nucleus of brain4.94e-189
basal ganglion5.24e-189
nuclear complex of neuraxis5.24e-189
aggregate regional part of brain5.24e-189
collection of basal ganglia5.24e-189
cerebral subcortex5.24e-189
organ system subdivision6.45e-17223
telencephalic nucleus3.01e-147
tube5.68e-14192
brainstem1.19e-126
gyrus3.32e-126
posterior neural tube4.06e-1215
chordal neural plate4.06e-1215
segmental subdivision of nervous system2.23e-1113
limbic system1.77e-105
temporal lobe2.42e-106
organ part4.64e-10218
segmental subdivision of hindbrain7.72e-1012
hindbrain7.72e-1012
presumptive hindbrain7.72e-1012
anatomical conduit1.58e-09240
corpus striatum9.14e-094
striatum9.14e-094
ventral part of telencephalon9.14e-094
future corpus striatum9.14e-094
regional part of diencephalon1.60e-084
anatomical cluster4.54e-08373
medulla oblongata2.39e-073
myelencephalon2.39e-073
future myelencephalon2.39e-073
caudate-putamen3.43e-073
dorsal striatum3.43e-073
diencephalon4.16e-077
future diencephalon4.16e-077
cell layer5.31e-07309
pons5.85e-073
occipital lobe6.49e-075
frontal cortex7.97e-073
epithelium8.44e-07306
parietal lobe9.02e-075


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)
MA0003.11.54338
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
MA0028.11.58389
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
MA0070.11.30033
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
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.11.55947
MA0103.10.628063
MA0105.10.846801
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.22.07011
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
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
CTBP2#1488241.81133355955210.0007543408259914850.00593465924864216
NR3C1#290829.982015554115360.01278474365547170.0460470339219164
SETDB1#9869226.8800174520070.001814468907964410.0108940108237364



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.