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Coexpression cluster:C3993

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Full id: C3993_dura_heart_Lymphatic_lung_acute_Fibroblast_pituitary



Phase1 CAGE Peaks

  Short description
Hg19::chr1:65990881..65990916,+ p5@LEPR
Hg19::chr1:65990922..65990927,+ p12@LEPR
Hg19::chr1:65990933..65990946,+ p8@LEPR


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
fibroblast of gingiva4.50e-075
Uber Anatomy
Ontology termp-valuen
adult organism3.05e-55114
neural tube9.83e-2256
neural rod9.83e-2256
future spinal cord9.83e-2256
neural keel9.83e-2256
regional part of nervous system8.88e-1953
regional part of brain8.88e-1953
neural plate4.58e-1782
presumptive neural plate4.58e-1782
neurectoderm1.05e-1586
structure with developmental contribution from neural crest2.54e-15132
regional part of forebrain2.64e-1541
forebrain2.64e-1541
anterior neural tube2.64e-1541
future forebrain2.64e-1541
central nervous system1.11e-1481
anatomical conduit2.01e-13240
brain grey matter2.17e-1334
gray matter2.17e-1334
brain2.76e-1368
future brain2.76e-1368
organ system subdivision3.45e-13223
telencephalon3.52e-1334
nervous system4.21e-1389
anatomical cluster7.18e-13373
regional part of telencephalon9.87e-1232
cerebral hemisphere1.20e-1132
ecto-epithelium5.65e-11104
ectoderm-derived structure7.19e-11171
ectoderm7.19e-11171
presumptive ectoderm7.19e-11171
basal ganglion5.91e-109
nuclear complex of neuraxis5.91e-109
aggregate regional part of brain5.91e-109
collection of basal ganglia5.91e-109
cerebral subcortex5.91e-109
pre-chordal neural plate6.38e-1061
neural nucleus8.12e-109
nucleus of brain8.12e-109
multi-tissue structure1.86e-09342
tube2.01e-08192
brainstem3.22e-086
regional part of cerebral cortex4.14e-0822
telencephalic nucleus8.04e-087
posterior neural tube1.00e-0715
chordal neural plate1.00e-0715
cerebral cortex8.88e-0725
pallium8.88e-0725


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
MA0014.10.377374
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.13.9895
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.110.4901
MA0074.12.15449
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
MA0105.14.18141
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.12.29491
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
MA0140.12.07172
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.11.98824
MA0149.10.884158
MA0062.20.449458
MA0035.22.07011
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.22.23118
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.12.08673
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.22.26143
MA0099.20.902716
MA0079.20.481578
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
E2F6#187635.017155731697390.00791769806886330.032264874502088
EGR1#195834.988179094810140.008056488137383440.0321002428116965
GATA1#2623313.56030814380040.0004009615963782630.00388244281143607
JUN#3725312.51282919233630.0005103313992726250.00444672960192172



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.