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Coexpression cluster:C4186

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Full id: C4186_retina_corpus_Retinal_medulla_eye_pons_spinal



Phase1 CAGE Peaks

  Short description
Hg19::chr2:219610834..219610846,+ p11@TTLL4
Hg19::chr2:219610848..219610865,+ p6@TTLL4
Hg19::chr2:219610868..219610888,+ p9@TTLL4


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
visual pigment cell2.40e-104
retinal pigment epithelial cell2.17e-083
Uber Anatomy
Ontology termp-valuen
neural tube9.29e-7956
neural rod9.29e-7956
future spinal cord9.29e-7956
neural keel9.29e-7956
regional part of nervous system7.26e-7253
regional part of brain7.26e-7253
neural plate5.92e-6782
presumptive neural plate5.92e-6782
central nervous system5.03e-6681
neurectoderm3.29e-6386
brain3.00e-6168
future brain3.00e-6168
nervous system7.81e-6189
regional part of forebrain2.64e-6041
forebrain2.64e-6041
anterior neural tube2.64e-6041
future forebrain2.64e-6041
telencephalon7.79e-5734
ecto-epithelium1.13e-56104
brain grey matter2.26e-5634
gray matter2.26e-5634
pre-chordal neural plate1.08e-5461
regional part of telencephalon5.91e-5232
cerebral hemisphere6.29e-5232
structure with developmental contribution from neural crest1.84e-43132
ectoderm-derived structure3.31e-40171
ectoderm3.31e-40171
presumptive ectoderm3.31e-40171
adult organism8.11e-39114
cerebral cortex1.94e-3625
pallium1.94e-3625
regional part of cerebral cortex2.48e-3422
neocortex2.69e-3020
organ system subdivision1.58e-23223
neural nucleus8.65e-229
nucleus of brain8.65e-229
tube1.32e-21192
basal ganglion1.41e-219
nuclear complex of neuraxis1.41e-219
aggregate regional part of brain1.41e-219
collection of basal ganglia1.41e-219
cerebral subcortex1.41e-219
posterior neural tube1.06e-1815
chordal neural plate1.06e-1815
telencephalic nucleus2.00e-177
epithelium6.16e-16306
brainstem1.23e-156
cell layer1.24e-15309
anatomical conduit1.96e-15240
segmental subdivision of nervous system1.63e-1413
anatomical cluster1.33e-13373
organ part9.69e-13218
segmental subdivision of hindbrain1.40e-1212
hindbrain1.40e-1212
presumptive hindbrain1.40e-1212
parietal lobe2.15e-125
limbic system2.15e-125
multi-tissue structure3.88e-11342
corpus striatum5.68e-114
striatum5.68e-114
ventral part of telencephalon5.68e-114
future corpus striatum5.68e-114
retina7.27e-116
photoreceptor array7.27e-116
posterior segment of eyeball7.27e-116
layer of retina1.43e-104
gyrus1.51e-106
temporal lobe7.26e-096
medulla oblongata8.74e-093
myelencephalon8.74e-093
future myelencephalon8.74e-093
organ1.43e-08503
pons1.53e-083
spinal cord1.61e-083
dorsal region element1.61e-083
dorsum1.61e-083
caudate-putamen1.65e-083
dorsal striatum1.65e-083
pigmented layer of retina2.17e-083
presumptive retinal pigmented epithelium2.17e-083
occipital lobe4.22e-085
germ layer1.89e-07560
germ layer / neural crest1.89e-07560
embryonic tissue1.89e-07560
presumptive structure1.89e-07560
germ layer / neural crest derived structure1.89e-07560
epiblast (generic)1.89e-07560
embryonic structure2.83e-07564
regional part of metencephalon8.39e-079
metencephalon8.39e-079
future metencephalon8.39e-079


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)
MA0003.10.708947
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.11.64148
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
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
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
MA0077.14.62358
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0114.11.35563
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
MA0145.10.752137
MA0146.11.70974
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
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
MA0154.10.312019
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
MA0079.20.0107199
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
EP300#203336.77394172622320.003216880500103790.016781607519997
FOSL2#2355316.93020060456170.0002060162053171620.00243505279166128
HDAC2#3066313.41562023662630.0004140761399857210.00392144522886912
HNF4A#3172323.13229036295378.07584663437677e-050.00123039146119282
HNF4G#3174328.75342252644684.20470658818262e-050.000758175675696141
RAD21#5885310.35503389545630.0009004912073565420.00665768095746212
SP1#666735.69838137814090.005403962701712170.0247103529161172
TCF7L2#6934310.77017656313730.0008003181298398380.00615224681012387



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.