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Coexpression cluster:C3155

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Full id: C3155_medulla_spinal_diencephalon_corpus_locus_globus_parietal



Phase1 CAGE Peaks

  Short description
Hg19::chr11:45922629..45922637,+ p@chr11:45922629..45922637
+
Hg19::chr17:76492734..76492735,+ p3@uc002jvt.1
Hg19::chr1:156589297..156589300,+ p9@HAPLN2


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:0005540hyaluronic acid binding0.0079477216531261
GO:0005539glycosaminoglycan binding0.00841133874955846
GO:0030247polysaccharide binding0.00841133874955846
GO:0001871pattern binding0.00841133874955846
GO:0005578proteinaceous extracellular matrix0.0211056163899682
GO:0030246carbohydrate binding0.0211056163899682
GO:0044421extracellular region part0.0282585658777817
GO:0022610biological adhesion0.0282585658777817
GO:0007155cell adhesion0.0282585658777817



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


uberon_data


Uber Anatomy
Ontology termp-valuen
neural tube1.60e-8056
neural rod1.60e-8056
future spinal cord1.60e-8056
neural keel1.60e-8056
regional part of nervous system7.05e-7253
regional part of brain7.05e-7253
brain1.92e-5968
future brain1.92e-5968
central nervous system1.58e-5881
neural plate5.20e-5482
presumptive neural plate5.20e-5482
nervous system2.16e-5289
neurectoderm2.46e-5186
regional part of forebrain4.07e-5141
forebrain4.07e-5141
anterior neural tube4.07e-5141
future forebrain4.07e-5141
brain grey matter1.18e-4834
gray matter1.18e-4834
telencephalon1.43e-4834
ecto-epithelium8.13e-42104
adult organism2.05e-41114
regional part of telencephalon2.87e-3932
cerebral hemisphere4.77e-3932
structure with developmental contribution from neural crest6.32e-35132
pre-chordal neural plate1.50e-3361
neocortex9.67e-3220
brainstem1.51e-306
posterior neural tube2.80e-3015
chordal neural plate2.80e-3015
regional part of cerebral cortex7.62e-2922
neural nucleus2.13e-289
nucleus of brain2.13e-289
ectoderm-derived structure1.12e-25171
ectoderm1.12e-25171
presumptive ectoderm1.12e-25171
cerebral cortex2.47e-2525
pallium2.47e-2525
pons2.43e-223
segmental subdivision of hindbrain1.50e-2112
hindbrain1.50e-2112
presumptive hindbrain1.50e-2112
tube8.80e-21192
organ system subdivision2.26e-20223
segmental subdivision of nervous system7.38e-2013
gyrus7.34e-196
telencephalic nucleus9.56e-177
anatomical conduit9.30e-16240
globus pallidus1.35e-152
pallidum1.35e-152
locus ceruleus1.80e-152
brainstem nucleus1.80e-152
hindbrain nucleus1.80e-152
middle temporal gyrus6.14e-152
parietal lobe1.64e-135
regional part of metencephalon4.27e-139
metencephalon4.27e-139
future metencephalon4.27e-139
basal ganglion4.55e-139
nuclear complex of neuraxis4.55e-139
aggregate regional part of brain4.55e-139
collection of basal ganglia4.55e-139
cerebral subcortex4.55e-139
epithelium2.14e-11306
cell layer3.06e-11309
medulla oblongata4.59e-113
myelencephalon4.59e-113
future myelencephalon4.59e-113
spinal cord6.47e-113
dorsal region element6.47e-113
dorsum6.47e-113
anatomical cluster1.91e-10373
organ part1.96e-10218
temporal lobe1.45e-096
corpus callosum8.15e-091
central nervous system cell part cluster8.15e-091
axon tract8.15e-091
intercerebral commissure8.15e-091
dorsal telencephalic commissure8.15e-091
brain white matter8.15e-091
brain commissure8.15e-091
white matter8.15e-091
nervous system commissure8.15e-091
cerebral hemisphere white matter8.15e-091
substantia nigra1.02e-081
midbrain nucleus1.02e-081
regional part of midbrain1.02e-081
midbrain1.02e-081
presumptive midbrain1.02e-081
midbrain neural tube1.02e-081
multi-tissue structure1.30e-08342
postcentral gyrus1.59e-081
olfactory region1.84e-081
primary subdivision of skull1.84e-081
cranium1.84e-081
neurocranium1.84e-081
chondrocranium1.84e-081
cartilaginous neurocranium1.84e-081
head paraxial mesoderm1.84e-081
occipital pole1.98e-081


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
MA0017.11.64148
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.12.16573
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.904546
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
MA0073.12.78116
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.11.77664
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
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.21.20011
MA0137.21.60005
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.22.97249
MA0150.10.744617
MA0151.10
MA0152.10.902317
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
MA0162.10.455568
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.90288
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


No analysis results for this cluster

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.