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Coexpression cluster:C2412

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Full id: C2412_neuroblastoma_cerebellum_Neurons_migratory_thalamus_parietal_amygdala



Phase1 CAGE Peaks

  Short description
Hg19::chr17:43861598..43861616,+ p4@CRHR1
Hg19::chr17:43861631..43861669,+ p2@CRHR1
Hg19::chr17:43861680..43861705,+ p1@CRHR1
Hg19::chr7:31726822..31726846,+ p1@PPP1R17


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:0015056corticotrophin-releasing factor receptor activity0.00264924055104203
GO:0001636corticotrophin-releasing factor gastric inhibitory peptide-like receptor activity0.00264924055104203
GO:0007567parturition0.00353232073472271
GO:0007190adenylate cyclase activation0.00463617096432356
GO:0031281positive regulation of cyclase activity0.00463617096432356
GO:0045762positive regulation of adenylate cyclase activity0.00463617096432356
GO:0051349positive regulation of lyase activity0.00463617096432356
GO:0007189G-protein signaling, adenylate cyclase activating pathway0.00463617096432356
GO:0001633secretin-like receptor activity0.00463617096432356
GO:0045761regulation of adenylate cyclase activity0.00463617096432356
GO:0031279regulation of cyclase activity0.00463617096432356
GO:0051339regulation of lyase activity0.00463617096432356
GO:0007565female pregnancy0.0076827975980219
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0076827975980219
GO:0019933cAMP-mediated signaling0.0076827975980219
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.00950609844785671
GO:0019935cyclic-nucleotide-mediated signaling0.00950609844785671
GO:0043085positive regulation of catalytic activity0.018684117570507
GO:0019932second-messenger-mediated signaling0.018684117570507
GO:0022414reproductive process0.0202004592016955
GO:0051704multi-organism process0.0210046929404047
GO:0050790regulation of catalytic activity0.036427057576828
GO:0065009regulation of a molecular function0.0386443567336784



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
embryonic stem cell5.19e-085
neuronal stem cell6.15e-088
Uber Anatomy
Ontology termp-valuen
central nervous system1.61e-7381
nervous system2.31e-6989
neural tube1.05e-6856
neural rod1.05e-6856
future spinal cord1.05e-6856
neural keel1.05e-6856
regional part of nervous system4.57e-6453
regional part of brain4.57e-6453
brain1.11e-5868
future brain1.11e-5868
regional part of forebrain4.23e-5341
forebrain4.23e-5341
anterior neural tube4.23e-5341
future forebrain4.23e-5341
neurectoderm2.94e-4986
neural plate1.83e-4882
presumptive neural plate1.83e-4882
adult organism1.50e-45114
telencephalon5.70e-4534
brain grey matter8.25e-4534
gray matter8.25e-4534
cerebral hemisphere7.48e-4232
regional part of telencephalon1.19e-4132
ecto-epithelium1.78e-38104
regional part of cerebral cortex1.02e-3622
pre-chordal neural plate2.64e-3661
ectoderm-derived structure4.24e-36171
ectoderm4.24e-36171
presumptive ectoderm4.24e-36171
cerebral cortex1.66e-3425
pallium1.66e-3425
neocortex1.84e-3320
structure with developmental contribution from neural crest3.88e-30132
organ system subdivision1.13e-27223
posterior neural tube4.16e-1615
chordal neural plate4.16e-1615
tube8.45e-15192
anatomical cluster2.47e-12373
segmental subdivision of hindbrain6.17e-1212
hindbrain6.17e-1212
presumptive hindbrain6.17e-1212
basal ganglion9.77e-129
nuclear complex of neuraxis9.77e-129
aggregate regional part of brain9.77e-129
collection of basal ganglia9.77e-129
cerebral subcortex9.77e-129
gyrus1.00e-116
neural nucleus1.34e-119
nucleus of brain1.34e-119
brainstem6.55e-116
segmental subdivision of nervous system7.49e-1113
anatomical conduit1.20e-10240
embryo3.83e-10592
parietal lobe5.34e-105
occipital lobe5.75e-105
temporal lobe5.83e-106
limbic system8.63e-105
diencephalon2.37e-097
future diencephalon2.37e-097
telencephalic nucleus1.34e-087
embryonic structure3.09e-08564
germ layer5.60e-08560
germ layer / neural crest5.60e-08560
embryonic tissue5.60e-08560
presumptive structure5.60e-08560
germ layer / neural crest derived structure5.60e-08560
epiblast (generic)5.60e-08560
developing anatomical structure9.54e-08581
regional part of metencephalon9.66e-089
metencephalon9.66e-089
future metencephalon9.66e-089
organ part1.62e-07218
epithelium3.19e-07306
multi-cellular organism4.55e-07656
cell layer5.13e-07309
testis8.54e-078
frontal cortex9.52e-073


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)
MA0003.11.8989
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.18.67501
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.11.8712
MA0056.10
MA0057.12.77736
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.866596
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.11.43218
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.13.19603
MA0146.11.75643
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.21.5472
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.21.7213
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.13.50007
MA0163.11.37853
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.218.3958
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
ZNF263#1012736.166381227758010.006539814347975980.0279693558840403



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.