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Coexpression cluster:C3447

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Full id: C3447_heart_left_skin_submaxillary_hippocampus_neuroblastoma_olfactory



Phase1 CAGE Peaks

  Short description
Hg19::chr14:69726342..69726428,+ p2@GALNTL1
Hg19::chr14:69726864..69726916,+ p1@GALNTL1
Hg19::chr14:69726920..69726925,+ p7@GALNTL1


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

cell_data
uberon_data


Cell Type
Ontology termp-valuen
neural cell4.12e-0825
Uber Anatomy
Ontology termp-valuen
central nervous system2.30e-5381
adult organism1.12e-51114
nervous system3.88e-5189
neural tube3.32e-4856
neural rod3.32e-4856
future spinal cord3.32e-4856
neural keel3.32e-4856
regional part of nervous system1.42e-4553
regional part of brain1.42e-4553
brain1.90e-4568
future brain1.90e-4568
neural plate2.60e-4182
presumptive neural plate2.60e-4182
neurectoderm3.47e-3986
regional part of forebrain5.30e-3641
forebrain5.30e-3641
anterior neural tube5.30e-3641
future forebrain5.30e-3641
organ system subdivision1.49e-34223
brain grey matter4.85e-3334
gray matter4.85e-3334
telencephalon8.83e-3334
cerebral hemisphere7.88e-3232
regional part of telencephalon3.53e-3132
ectoderm-derived structure1.12e-30171
ectoderm1.12e-30171
presumptive ectoderm1.12e-30171
structure with developmental contribution from neural crest2.38e-29132
ecto-epithelium4.44e-29104
pre-chordal neural plate9.78e-2861
cerebral cortex1.14e-2525
pallium1.14e-2525
anatomical cluster1.67e-24373
regional part of cerebral cortex4.24e-2322
neocortex3.61e-2120
multi-tissue structure1.11e-17342
organ part2.58e-14218
posterior neural tube5.76e-1315
chordal neural plate5.76e-1315
tube3.34e-12192
organ2.90e-11503
anatomical conduit4.96e-11240
multi-cellular organism1.13e-10656
embryo1.44e-10592
segmental subdivision of hindbrain1.52e-1012
hindbrain1.52e-1012
presumptive hindbrain1.52e-1012
epithelium7.88e-10306
cell layer1.90e-09309
segmental subdivision of nervous system2.04e-0913
basal ganglion4.36e-099
nuclear complex of neuraxis4.36e-099
aggregate regional part of brain4.36e-099
collection of basal ganglia4.36e-099
cerebral subcortex4.36e-099
developing anatomical structure4.88e-09581
neural nucleus8.98e-099
nucleus of brain8.98e-099
regional part of metencephalon1.34e-089
metencephalon1.34e-089
future metencephalon1.34e-089
anatomical system2.44e-08624
temporal lobe2.90e-086
anatomical group3.03e-08625
germ layer6.29e-08560
germ layer / neural crest6.29e-08560
embryonic tissue6.29e-08560
presumptive structure6.29e-08560
germ layer / neural crest derived structure6.29e-08560
epiblast (generic)6.29e-08560
embryonic structure6.98e-08564
gyrus1.87e-076
telencephalic nucleus5.55e-077


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)
MA0003.13.22681
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
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
MA0042.11.89908
MA0043.11.32783
MA0046.11.31611
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.06172
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
MA0073.15.1975
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
MA0119.11.66081
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
MA0140.12.07172
MA0141.11.6959
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.12.11725
MA0146.10.707589
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
MA0112.20.264678
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
MA0159.12.37721
MA0160.10.871361
MA0161.10
MA0162.12.05956
MA0163.13.19905
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.23.61229
MA0102.21.88331
MA0258.11.29138
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
CTCF#1066435.360256373075030.0064925092527670.0278915377339366
CTCFL#140690213.16431623931620.007433367036996010.030671779857644



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.