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Coexpression cluster:C3088

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Full id: C3088_duodenum_medial_temporal_olfactory_amygdala_occipital_spinal



Phase1 CAGE Peaks

Hg19::chr11:117712544..117712563,-p@chr11:117712544..117712563
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Hg19::chr2:149806933..149806951,+p@chr2:149806933..149806951
+
Hg19::chr2:55254388..55254405,-p@chr2:55254388..55254405
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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><br>


Cell Type
Ontology termp-valuen
neuron3.57e-096
neuroblast3.57e-096
electrically signaling cell3.57e-096
neuronal stem cell4.46e-098
neural cell1.18e-0825
Uber Anatomy
Ontology termp-valuen
nervous system6.35e-6389
central nervous system1.22e-6081
neural tube9.79e-5956
neural rod9.79e-5956
future spinal cord9.79e-5956
neural keel9.79e-5956
regional part of nervous system1.70e-5453
regional part of brain1.70e-5453
regional part of forebrain6.09e-4941
forebrain6.09e-4941
anterior neural tube6.09e-4941
future forebrain6.09e-4941
brain3.53e-4668
future brain3.53e-4668
brain grey matter4.78e-4534
gray matter4.78e-4534
neural plate6.18e-4582
presumptive neural plate6.18e-4582
telencephalon8.03e-4534
neurectoderm1.08e-4386
regional part of telencephalon4.14e-4232
cerebral hemisphere4.39e-4232
pre-chordal neural plate2.86e-3761
cerebral cortex1.02e-3525
pallium1.02e-3525
ecto-epithelium1.28e-34104
ectoderm-derived structure1.89e-34171
ectoderm1.89e-34171
presumptive ectoderm1.89e-34171
regional part of cerebral cortex2.66e-3222
structure with developmental contribution from neural crest4.04e-30132
adult organism6.95e-30114
neocortex2.73e-2920
organ system subdivision2.05e-21223
posterior neural tube3.81e-1115
chordal neural plate3.81e-1115
basal ganglion5.58e-119
nuclear complex of neuraxis5.58e-119
aggregate regional part of brain5.58e-119
collection of basal ganglia5.58e-119
cerebral subcortex5.58e-119
neural nucleus1.02e-109
nucleus of brain1.02e-109
gyrus1.40e-106
tube1.99e-10192
embryo2.41e-10592
anatomical cluster1.85e-09373
brainstem2.49e-096
temporal lobe4.27e-096
parietal lobe5.98e-095
occipital lobe6.08e-095
embryonic structure6.18e-09564
limbic system6.80e-095
segmental subdivision of nervous system8.32e-0913
germ layer9.75e-09560
germ layer / neural crest9.75e-09560
embryonic tissue9.75e-09560
presumptive structure9.75e-09560
germ layer / neural crest derived structure9.75e-09560
epiblast (generic)9.75e-09560
organ part1.11e-08218
developing anatomical structure3.17e-08581
multi-cellular organism4.99e-08656
telencephalic nucleus5.86e-087
segmental subdivision of hindbrain1.39e-0712
hindbrain1.39e-0712
presumptive hindbrain1.39e-0712
anatomical system6.81e-07624
anatomical group7.79e-07625


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
MA0014.10.118426
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
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
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
MA0114.10.549955
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
MA0140.10.894983
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
MA0039.20.0526989
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
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.12.37721
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0373086
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.