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Coexpression cluster:C1005: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.348717,0.0704539,0.341646,1.21028,0.301904,0.480078,0.554663,0.19223,0.190005,0.637689,1.14354,0.597407,0.907465,0.543352,0.300614,0.322799,0.774423,0.250594,0.491486,0.560708,0.341703,0.047825,0.472508,0.29709,0.385586,0.619829,1.34894,1.18607,0.304828,0.122648,0.429397,0.810962,0.220667,0.469827,0.269459,0.0649851,0.735464,0.481208,0.244807,2.25462,0.268162,0.413601,0.201367,0.299183,0.198862,0.371118,1.36786,0.440085,0.186577,0.304949,0.63387,1.39237,0.309329,0.887323,1.03948,1.34776,0.831988,0.514077,0.122557,1.27736,0.85167,0.558065,0.190442,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.197328,0.0911419,1.03748,0.149081,1.36791,0.127753,0.730167,0.797419,0.379656,0.50159,0.745864,0.575394,0.19474,0.986227,0.237806,8.91454,0.759942,0.659621,1.59442,1.22073,0.959334,1.93366,1.87422,0.302606,0.239285,0.946574,0.87,0.664183,0.106284,1.27523,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,1.00159,0.286892,0.92894,0.861701,2.42894,0.459808,1.17281,0.265019,0.279527,5.0151,0.710479,0.229841,1.02923,0.657218,2.08588,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,0.113443,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,0.224241,0.0833399,2.1277,0.960402,0.183004,0.557588,1.36372,0.643609,2.19336,0.385642,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,1.15008,0.553354,0.0203307
|tfbs_overrepresentation_for_novel_motifs=0.348717,0.0704539,0.341646,1.21028,0.301904,0.480078,0.554663,0.19223,0.190005,0.637689,1.14354,0.597407,0.907465,0.543352,0.300614,0.322799,0.774423,0.250594,0.491486,0.560708,0.341703,0.047825,0.472508,0.29709,0.385586,0.619829,1.34894,1.18607,0.304828,0.122648,0.429397,0.810962,0.220667,0.469827,0.269459,0.0649851,0.735464,0.481208,0.244807,2.25462,0.268162,0.413601,0.201367,0.299183,0.198862,0.371118,1.36786,0.440085,0.186577,0.304949,0.63387,1.39237,0.309329,0.887323,1.03948,1.34776,0.831988,0.514077,0.122557,1.27736,0.85167,0.558065,0.190442,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.197328,0.0911419,1.03748,0.149081,1.36791,0.127753,0.730167,0.797419,0.379656,0.50159,0.745864,0.575394,0.19474,0.986227,0.237806,8.91454,0.759942,0.659621,1.59442,1.22073,0.959334,1.93366,1.87422,0.302606,0.239285,0.946574,0.87,0.664183,0.106284,1.27523,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,1.00159,0.286892,0.92894,0.861701,2.42894,0.459808,1.17281,0.265019,0.279527,5.0151,0.710479,0.229841,1.02923,0.657218,2.08588,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,0.113443,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,0.224241,0.0833399,2.1277,0.960402,0.183004,0.557588,1.36372,0.643609,2.19336,0.385642,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,1.15008,0.553354,0.0203307
|tfbs_overrepresentation_jaspar=MA0003.1;0.00101002,MA0004.1;0.455723,MA0006.1;0.812175,MA0007.1;0.437331,MA0009.1;0.918715,MA0014.1;0.00962431,MA0017.1;0.337901,MA0019.1;0.602411,MA0024.1;0.813542,MA0025.1;1.05265,MA0027.1;2.5321,MA0028.1;0.315574,MA0029.1;0.832916,MA0030.1;0.821423,MA0031.1;0.756713,MA0038.1;0.557409,MA0040.1;0.838784,MA0041.1;0.474018,MA0042.1;0.442535,MA0043.1;0.919032,MA0046.1;0.90778,MA0048.1;0.0955945,MA0050.1;0.443405,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;0.028436,MA0056.1;0,MA0057.1;0.305162,MA0058.1;0.362328,MA0059.1;0.361075,MA0060.1;0.190336,MA0061.1;0.165998,MA0063.1;0,MA0066.1;0.557833,MA0067.1;1.23721,MA0068.1;0.133123,MA0069.1;2.08998,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;0.466265,MA0074.1;0.552456,MA0076.1;0.377799,MA0077.1;0.880402,MA0078.1;0.652193,MA0081.1;0.948525,MA0083.1;0.926258,MA0084.1;1.42483,MA0087.1;0.885691,MA0088.1;0.441522,MA0089.1;0,MA0090.1;0.391903,MA0091.1;0.458301,MA0092.1;0.421159,MA0093.1;0.303084,MA0095.1;0,MA0098.1;0,MA0100.1;0.571227,MA0101.1;0.30624,MA0103.1;0.291333,MA0105.1;0.0818021,MA0106.1;0.59853,MA0107.1;0.236528,MA0108.2;0.753643,MA0109.1;0,MA0111.1;0.405141,MA0113.1;0.614917,MA0114.1;0.231781,MA0115.1;1.1606,MA0116.1;0.239768,MA0117.1;0.956472,MA0119.1;0.345493,MA0122.1;0.982472,MA0124.1;1.11898,MA0125.1;1.0347,MA0130.1;0,MA0131.1;0.670358,MA0132.1;0,MA0133.1;0,MA0135.1;0.949204,MA0136.1;0.564434,MA0139.1;0.155155,MA0140.1;0.516266,MA0141.1;0.359385,MA0142.1;0.724856,MA0143.1;1.49284,MA0144.1;1.82745,MA0145.1;0.830366,MA0146.1;0.00761723,MA0147.1;0.243042,MA0148.1;0.480298,MA0149.1;0.506665,MA0062.2;0.161302,MA0035.2;0.515566,MA0039.2;0.0817047,MA0138.2;0.653421,MA0002.2;0.179788,MA0137.2;0.321796,MA0104.2;0.189646,MA0047.2;0.586412,MA0112.2;0.0572179,MA0065.2;0.0631316,MA0150.1;0.386144,MA0151.1;0,MA0152.1;0.52279,MA0153.1;1.01778,MA0154.1;0.577214,MA0155.1;0.0535085,MA0156.1;0.323987,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.243637,MA0160.1;1.23953,MA0161.1;0,MA0162.1;0.378102,MA0163.1;0.0104024,MA0164.1;1.51849,MA0080.2;0.303167,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;0.13841,MA0102.2;1.46209,MA0258.1;0.209744,MA0259.1;0.699589,MA0442.1;0
}}
}}

Revision as of 19:37, 22 January 2013


Full id: C1005_nonsmall_cerebellum_spinal_medulla_locus_small_thalamus



Phase1 CAGE Peaks

Hg19::chr11:82556854..82556872,-p3@PRCP
Hg19::chr12:41221946..41221953,+p16@CNTN1
Hg19::chr12:41221975..41221996,+p2@CNTN1
Hg19::chr12:41222004..41222020,+p4@CNTN1
Hg19::chr18:32073253..32073339,+p2@DTNA
Hg19::chr18:32073350..32073378,+p6@DTNA
Hg19::chr18:32073391..32073409,+p9@DTNA
Hg19::chr18:32073414..32073417,+p18@DTNA


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

GO IDGO nameFDR corrected p-value
GO:0008322Pro-X carboxypeptidase activity0.0027375485694101
GO:0004188serine-type Pro-X carboxypeptidase activity0.0027375485694101
GO:0007274neuromuscular synaptic transmission0.0150520853554045
GO:0004185serine carboxypeptidase activity0.0150520853554045
GO:0006941striated muscle contraction0.0404727979551289
GO:0007219Notch signaling pathway0.0455600295114098



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube6.92e-8456
neural rod6.92e-8456
future spinal cord6.92e-8456
neural keel6.92e-8456
central nervous system1.50e-8181
nervous system6.07e-8089
regional part of nervous system1.99e-7753
regional part of brain1.99e-7753
brain3.65e-7068
future brain3.65e-7068
adult organism1.77e-66114
neural plate6.04e-6582
presumptive neural plate6.04e-6582
regional part of forebrain6.54e-6341
forebrain6.54e-6341
anterior neural tube6.54e-6341
future forebrain6.54e-6341
neurectoderm3.41e-6186
brain grey matter1.33e-5334
gray matter1.33e-5334
telencephalon2.83e-5334
ecto-epithelium7.87e-52104
cerebral hemisphere2.48e-4932
regional part of telencephalon2.52e-4932
pre-chordal neural plate7.97e-4661
ectoderm-derived structure4.52e-45171
ectoderm4.52e-45171
presumptive ectoderm4.52e-45171
regional part of cerebral cortex1.34e-4122
structure with developmental contribution from neural crest9.98e-41132
neocortex1.87e-3720
organ system subdivision3.86e-36223
cerebral cortex5.52e-3625
pallium5.52e-3625
tube7.29e-24192
anatomical cluster7.11e-23373
posterior neural tube5.29e-2115
chordal neural plate5.29e-2115
anatomical conduit3.26e-19240
neural nucleus3.75e-199
nucleus of brain3.75e-199
basal ganglion5.04e-199
nuclear complex of neuraxis5.04e-199
aggregate regional part of brain5.04e-199
collection of basal ganglia5.04e-199
cerebral subcortex5.04e-199
segmental subdivision of nervous system7.73e-1713
segmental subdivision of hindbrain3.88e-1512
hindbrain3.88e-1512
presumptive hindbrain3.88e-1512
telencephalic nucleus6.44e-157
epithelium8.01e-15306
brainstem1.46e-146
cell layer1.65e-14309
multi-tissue structure1.20e-13342
gyrus2.29e-136
organ part1.30e-12218
limbic system9.17e-125
embryo2.45e-11592
temporal lobe2.78e-116
parietal lobe3.77e-115
diencephalon8.97e-117
future diencephalon8.97e-117
developing anatomical structure9.84e-11581
occipital lobe1.07e-105
germ layer3.26e-10560
germ layer / neural crest3.26e-10560
embryonic tissue3.26e-10560
presumptive structure3.26e-10560
germ layer / neural crest derived structure3.26e-10560
epiblast (generic)3.26e-10560
embryonic structure5.50e-10564
organ1.19e-09503
regional part of metencephalon2.73e-099
metencephalon2.73e-099
future metencephalon2.73e-099
regional part of diencephalon2.86e-094
corpus striatum3.38e-094
striatum3.38e-094
ventral part of telencephalon3.38e-094
future corpus striatum3.38e-094
multi-cellular organism3.93e-09656
anatomical system4.99e-09624
anatomical group5.61e-09625
medulla oblongata3.45e-083
myelencephalon3.45e-083
future myelencephalon3.45e-083
pons4.74e-083
spinal cord7.41e-083
dorsal region element7.41e-083
dorsum7.41e-083
frontal cortex1.70e-073
caudate-putamen2.56e-073
dorsal striatum2.56e-073


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
MA0006.10.812175
MA0007.10.437331
MA0009.10.918715
MA0014.10.00962431
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
MA0069.12.08998
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.466265
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.948525
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.441522
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
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
MA0141.10.359385
MA0142.10.724856
MA0143.11.49284
MA0144.11.82745
MA0145.10.830366
MA0146.10.00761723
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.0817047
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.0572179
MA0065.20.0631316
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.577214
MA0155.10.0535085
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.11.23953
MA0161.10
MA0162.10.378102
MA0163.10.0104024
MA0164.11.51849
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.13841
MA0102.21.46209
MA0258.10.209744
MA0259.10.699589
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
EBF1#187944.45323342328450.007651884996748980.0315149151027473
FOS#235344.49897765444720.007374489916227120.0304794155827632
GATA2#262446.3724658667770.002048740757051450.0118937429641855
GATA3#2625413.6182581786030.0001128396522810840.00154656961215015
JUN#372546.256414596168170.0021942117541140.0126454740860784
MAFF#23764321.11825868372940.0002930101691141860.00310771697492805
MAFK#7975310.16277492668620.002445573107139520.01376742182711
TRIM28#1015549.295262522631260.0004914980333421480.00439332104623593
USF2#739246.49609869253480.001906760815928170.0112204300684428



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1005&oldid=2569516"