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Coexpression cluster:C4021

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Full id: C4021_spinal_CD14_substantia_optic_medulla_locus_thalamus



Phase1 CAGE Peaks

  Short description
Hg19::chr20:24951811..24951815,- p@chr20:24951811..24951815
-
Hg19::chr5:42812123..42812140,- p10@SEPP1
Hg19::chr5:42812143..42812169,- p3@SEPP1


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
adult endothelial progenitor cell1.53e-073
Uber Anatomy
Ontology termp-valuen
adult organism6.48e-83114
neural tube1.06e-3956
neural rod1.06e-3956
future spinal cord1.06e-3956
neural keel1.06e-3956
regional part of nervous system6.07e-3553
regional part of brain6.07e-3553
regional part of forebrain2.04e-2841
forebrain2.04e-2841
anterior neural tube2.04e-2841
future forebrain2.04e-2841
neural plate2.27e-2882
presumptive neural plate2.27e-2882
central nervous system3.34e-2881
neurectoderm5.94e-2886
brain3.41e-2668
future brain3.41e-2668
nervous system7.12e-2689
brain grey matter3.16e-2534
gray matter3.16e-2534
telencephalon4.54e-2534
regional part of telencephalon5.49e-2232
cerebral hemisphere7.76e-2232
ecto-epithelium6.56e-21104
organ system subdivision1.16e-19223
pre-chordal neural plate1.42e-1961
regional part of cerebral cortex3.68e-1722
structure with developmental contribution from neural crest6.06e-17132
neocortex1.45e-1620
cerebral cortex1.16e-1425
pallium1.16e-1425
tube2.24e-13192
neural nucleus3.41e-139
nucleus of brain3.41e-139
brainstem6.01e-136
posterior neural tube3.26e-1215
chordal neural plate3.26e-1215
ectoderm-derived structure4.38e-12171
ectoderm4.38e-12171
presumptive ectoderm4.38e-12171
anatomical conduit1.51e-11240
anatomical cluster1.72e-11373
organ2.02e-10503
multi-tissue structure5.68e-10342
basal ganglion1.39e-099
nuclear complex of neuraxis1.39e-099
aggregate regional part of brain1.39e-099
collection of basal ganglia1.39e-099
cerebral subcortex1.39e-099
telencephalic nucleus1.67e-097
segmental subdivision of nervous system2.76e-0913
developing anatomical structure7.61e-08581
segmental subdivision of hindbrain1.01e-0712
hindbrain1.01e-0712
presumptive hindbrain1.01e-0712
embryo1.02e-07592
germ layer1.13e-07560
germ layer / neural crest1.13e-07560
embryonic tissue1.13e-07560
presumptive structure1.13e-07560
germ layer / neural crest derived structure1.13e-07560
epiblast (generic)1.13e-07560
gyrus1.80e-076
embryonic structure1.85e-07564
pons2.35e-073
medulla oblongata3.00e-073
myelencephalon3.00e-073
future myelencephalon3.00e-073
spinal cord4.56e-073
dorsal region element4.56e-073
dorsum4.56e-073
epithelium6.84e-07306
organ part7.18e-07218
multi-cellular organism7.47e-07656


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
MA0014.10.118426
MA0017.12.76432
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.14.43519
MA0031.12.60497
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
MA0101.10.646932
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
MA0141.11.6959
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
MA0035.20.894194
MA0039.20.0526989
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
MA0157.14.03241
MA0158.10
MA0159.10.565904
MA0160.12.02335
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.09178
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
BHLHE40#8553229.91454236465160.001467483527106140.00939799559035067
ESRRA#21012322.5602094240841.27639599649441e-050.000313144283481041
FOSL2#2355211.28680040304110.0100534586973120.0376793645621389
FOXA2#3170216.42030916844350.004810682352105480.0225940034254416
GATA3#2625218.15767757147070.003944546819279620.018953097407929
HNF4A#3172215.42152690863580.005444210486686610.0246772231682246
HNF4G#3174219.16894835096450.003543986611284220.0179736035398394
MAFF#23764237.54357099329680.0009344774015560320.00676996984885616
MAFK#7975218.06715542521990.003983674744936810.0191129642909985
RXRA#6256213.38307809275550.007196434429465730.0298332241249145
TRIM28#10155212.39368336350830.008368344129438470.0329183236359482



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.