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Coexpression cluster:C1544: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;2.58181,MA0004.1;0.558729,MA0006.1;1.01439,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;1.149,MA0017.1;0.432438,MA0019.1;1.69574,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;1.45353,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;1.71708,MA0056.1;0,MA0057.1;0.450439,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.578694,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.00563817,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;1.15882,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;0.32124,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.134725,MA0106.1;0.70837,MA0107.1;0.857383,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;0.323925,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;2.62599,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;1.16614,MA0146.1;1.05598,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;0.0313803,MA0138.2;3.01409,MA0002.2;0.709311,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;0.332548,MA0065.2;0.109623,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;1.3291,MA0155.1;0.0961854,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;1.39622,MA0163.1;0.273773,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.792956,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 20:00, 22 January 2013


Full id: C1544_caudate_globus_optic_locus_spinal_hippocampus_thalamus



Phase1 CAGE Peaks

Hg19::chr8:68864042..68864056,+p11@PREX2
Hg19::chr8:68864487..68864512,+p4@PREX2
Hg19::chr8:68864580..68864596,+p5@PREX2
Hg19::chr8:68864598..68864664,+p1@PREX2
Hg19::chr8:68864670..68864683,+p14@PREX2
Hg19::chr8:69143730..69143734,+p@chr8:69143730..69143734
+


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>

Uber Anatomy
Ontology termp-valuen
adult organism3.73e-63114
neural tube6.20e-5256
neural rod6.20e-5256
future spinal cord6.20e-5256
neural keel6.20e-5256
central nervous system5.21e-5181
regional part of nervous system1.58e-4853
regional part of brain1.58e-4853
nervous system1.53e-4689
regional part of forebrain2.01e-4041
forebrain2.01e-4041
anterior neural tube2.01e-4041
future forebrain2.01e-4041
brain2.32e-3968
future brain2.32e-3968
neural plate2.19e-3782
presumptive neural plate2.19e-3782
neurectoderm1.33e-3486
brain grey matter4.04e-3434
gray matter4.04e-3434
telencephalon7.58e-3434
regional part of telencephalon7.88e-3232
cerebral hemisphere1.07e-3132
pre-chordal neural plate4.94e-2661
ecto-epithelium6.91e-26104
cerebral cortex6.72e-2425
pallium6.72e-2425
structure with developmental contribution from neural crest4.29e-23132
anatomical cluster4.81e-23373
regional part of cerebral cortex6.59e-2222
anatomical conduit1.49e-21240
tube3.15e-21192
organ system subdivision3.46e-21223
ectoderm-derived structure1.25e-20171
ectoderm1.25e-20171
presumptive ectoderm1.25e-20171
neocortex1.46e-1920
posterior neural tube2.40e-1215
chordal neural plate2.40e-1215
neural nucleus1.07e-119
nucleus of brain1.07e-119
basal ganglion1.20e-119
nuclear complex of neuraxis1.20e-119
aggregate regional part of brain1.20e-119
collection of basal ganglia1.20e-119
cerebral subcortex1.20e-119
blood vessel endothelium6.01e-1118
endothelium6.01e-1118
cardiovascular system endothelium6.01e-1118
segmental subdivision of nervous system2.24e-1013
epithelium1.12e-09306
telencephalic nucleus1.83e-097
cell layer2.45e-09309
segmental subdivision of hindbrain2.83e-0912
hindbrain2.83e-0912
presumptive hindbrain2.83e-0912
embryo1.49e-08592
brainstem2.63e-086
simple squamous epithelium3.98e-0822
multi-cellular organism4.68e-08656
diencephalon6.94e-087
future diencephalon6.94e-087
temporal lobe7.74e-086
gyrus1.76e-076
limbic system2.96e-075
anatomical system6.86e-07624
organ part7.64e-07218
anatomical group8.16e-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)
MA0003.12.58181
MA0004.10.558729
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.11.149
MA0017.10.432438
MA0019.11.69574
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.11.45353
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.11.71708
MA0056.10
MA0057.10.450439
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00563817
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.11.15882
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.32124
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.12.62599
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.11.16614
MA0146.11.05598
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.0313803
MA0138.23.01409
MA0002.20.709311
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.332548
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.11.3291
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.11.39622
MA0163.10.273773
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.792956
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCF#1066443.573504248716680.01316635007238510.0466160565194193



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.

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