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Coexpression cluster:C1084

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Full id: C1084_cerebellum_iPS_HES3GFP_nonsmall_occipital_parietal_caudate



Phase1 CAGE Peaks

Hg19::chr4:93224865..93224903,+p@chr4:93224865..93224903
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Hg19::chr4:93224904..93224918,+p@chr4:93224904..93224918
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Hg19::chr4:93329615..93329616,+p@chr4:93329615..93329616
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Hg19::chr4:93520199..93520202,+p@chr4:93520199..93520202
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Hg19::chr4:93587821..93587823,+p@chr4:93587821..93587823
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Hg19::chr4:93706240..93706244,+p@chr4:93706240..93706244
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Hg19::chr4:93851749..93851753,+p@chr4:93851749..93851753
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Hg19::chr4:94044063..94044065,+p@chr4:94044063..94044065
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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
embryonic stem cell1.46e-135
neuron1.51e-086
neuroblast1.51e-086
electrically signaling cell1.51e-086
Uber Anatomy
Ontology termp-valuen
neural tube2.12e-7556
neural rod2.12e-7556
future spinal cord2.12e-7556
neural keel2.12e-7556
central nervous system7.24e-6981
regional part of nervous system8.61e-6853
regional part of brain8.61e-6853
nervous system6.98e-6189
brain1.65e-5568
future brain1.65e-5568
brain grey matter5.66e-5334
gray matter5.66e-5334
telencephalon1.82e-5234
neural plate9.96e-5182
presumptive neural plate9.96e-5182
neurectoderm2.53e-5086
regional part of forebrain1.15e-4941
forebrain1.15e-4941
anterior neural tube1.15e-4941
future forebrain1.15e-4941
regional part of telencephalon7.13e-4832
cerebral hemisphere1.26e-4732
ecto-epithelium1.01e-39104
regional part of cerebral cortex2.03e-3522
neocortex1.22e-3420
pre-chordal neural plate2.82e-3361
adult organism5.82e-33114
cerebral cortex9.18e-3125
pallium9.18e-3125
ectoderm-derived structure2.10e-30171
ectoderm2.10e-30171
presumptive ectoderm2.10e-30171
structure with developmental contribution from neural crest4.76e-29132
posterior neural tube2.71e-2615
chordal neural plate2.71e-2615
neural nucleus1.82e-259
nucleus of brain1.82e-259
organ system subdivision5.73e-23223
telencephalic nucleus3.72e-207
basal ganglion3.93e-209
nuclear complex of neuraxis3.93e-209
aggregate regional part of brain3.93e-209
collection of basal ganglia3.93e-209
cerebral subcortex3.93e-209
segmental subdivision of hindbrain8.72e-1912
hindbrain8.72e-1912
presumptive hindbrain8.72e-1912
tube1.31e-17192
segmental subdivision of nervous system3.41e-1713
brainstem6.26e-176
parietal lobe4.33e-145
corpus striatum1.99e-124
striatum1.99e-124
ventral part of telencephalon1.99e-124
future corpus striatum1.99e-124
anatomical conduit6.56e-12240
regional part of metencephalon8.13e-129
metencephalon8.13e-129
future metencephalon8.13e-129
gyrus2.19e-116
anatomical cluster1.54e-10373
organ part5.88e-10218
temporal lobe6.40e-106
caudate-putamen6.71e-103
dorsal striatum6.71e-103
spinal cord1.27e-093
dorsal region element1.27e-093
dorsum1.27e-093
pons2.33e-093
occipital lobe2.44e-095
medulla oblongata2.84e-093
myelencephalon2.84e-093
future myelencephalon2.84e-093
epithelium7.12e-09306
cell layer1.11e-08309
embryo1.07e-07592
caudate nucleus4.61e-072
future caudate nucleus4.61e-072
locus ceruleus5.34e-072
brainstem nucleus5.34e-072
hindbrain nucleus5.34e-072


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)
MA0003.10.00101002
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.0484929
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.0955945
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.028436
MA0056.10
MA0057.10.305162
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.19.20286e-05
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.054222
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.825856
MA0103.10.291333
MA0105.10.0818021
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.10.944441
MA0142.11.72156
MA0143.11.49284
MA0144.10.218541
MA0145.10.0613434
MA0146.10.00761723
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.21.28264
MA0039.20.00133745
MA0138.20.653421
MA0002.20.179788
MA0137.20.86081
MA0104.20.55506
MA0047.20.586412
MA0112.20.0572179
MA0065.20.0631316
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.0799828
MA0155.10.0535085
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.0163939
MA0163.10.0104024
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.21.80475e-05
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
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.