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Coexpression cluster:C3749

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Full id: C3749_brain_Neurons_parietal_occipital_temporal_cerebellum_medial



Phase1 CAGE Peaks

Hg19::chr19:11562404..11562424,-p@chr19:11562404..11562424
-
Hg19::chr2:27170763..27170781,+p5@DPYSL5
Hg19::chr8:80577410..80577417,+p@chr8:80577410..80577417
+


Enriched pathways on this co-expression cluster<b>Summary:</b><br>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.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>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. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>


Cell Type
Ontology termp-valuen
Merkel cell2.72e-072
Uber Anatomy
Ontology termp-valuen
neural tube2.03e-7756
neural rod2.03e-7756
future spinal cord2.03e-7756
neural keel2.03e-7756
central nervous system1.82e-7581
nervous system4.09e-7389
regional part of nervous system1.63e-6953
regional part of brain1.63e-6953
brain1.31e-6468
future brain1.31e-6468
neurectoderm7.87e-5886
neural plate2.09e-5582
presumptive neural plate2.09e-5582
regional part of forebrain9.65e-5541
forebrain9.65e-5541
anterior neural tube9.65e-5541
future forebrain9.65e-5541
brain grey matter3.30e-5334
gray matter3.30e-5334
telencephalon5.64e-5334
regional part of telencephalon7.43e-4832
cerebral hemisphere2.21e-4732
ecto-epithelium2.83e-46104
ectoderm-derived structure2.65e-41171
ectoderm2.65e-41171
presumptive ectoderm2.65e-41171
pre-chordal neural plate8.25e-4061
regional part of cerebral cortex6.10e-3922
neocortex1.51e-3820
cerebral cortex7.00e-3425
pallium7.00e-3425
structure with developmental contribution from neural crest3.41e-32132
adult organism6.00e-31114
organ system subdivision6.06e-30223
posterior neural tube8.64e-2315
chordal neural plate8.64e-2315
neural nucleus2.42e-219
nucleus of brain2.42e-219
tube1.26e-18192
brainstem5.04e-186
gyrus7.01e-186
basal ganglion2.52e-169
nuclear complex of neuraxis2.52e-169
aggregate regional part of brain2.52e-169
collection of basal ganglia2.52e-169
cerebral subcortex2.52e-169
telencephalic nucleus8.54e-167
segmental subdivision of hindbrain2.46e-1512
hindbrain2.46e-1512
presumptive hindbrain2.46e-1512
segmental subdivision of nervous system4.81e-1413
anatomical cluster1.57e-13373
anatomical conduit8.52e-13240
organ part3.41e-11218
temporal lobe3.64e-116
epithelium1.33e-10306
cell layer2.15e-10309
occipital lobe2.59e-105
parietal lobe3.54e-105
spinal cord5.74e-103
dorsal region element5.74e-103
dorsum5.74e-103
medulla oblongata5.92e-103
myelencephalon5.92e-103
future myelencephalon5.92e-103
pons8.79e-103
frontal cortex9.91e-103
regional part of metencephalon1.90e-089
metencephalon1.90e-089
future metencephalon1.90e-089
embryo8.22e-08592
dorsal plus ventral thalamus1.16e-072
thalamic complex1.16e-072
corpus striatum1.38e-074
striatum1.38e-074
ventral part of telencephalon1.38e-074
future corpus striatum1.38e-074
locus ceruleus2.40e-072
brainstem nucleus2.40e-072
hindbrain nucleus2.40e-072
germ layer2.78e-07560
germ layer / neural crest2.78e-07560
embryonic tissue2.78e-07560
presumptive structure2.78e-07560
germ layer / neural crest derived structure2.78e-07560
epiblast (generic)2.78e-07560
middle temporal gyrus2.80e-072
middle frontal gyrus2.98e-072
globus pallidus3.48e-072
pallidum3.48e-072
embryonic structure3.92e-07564
multi-tissue structure4.83e-07342
Disease
Ontology termp-valuen
lung small cell carcinoma9.98e-074


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>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. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>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
MA0038.10.94098
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
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.14.54482
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
MA0092.11.84783
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
MA0115.11.57693
MA0116.11.3784
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
MA0145.10.273764
MA0146.12.3244
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.22.97249
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.10.711948
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
MA0018.20.987913
MA0099.20.902716
MA0079.24.62164
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.