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Coexpression cluster:C1030: Difference between revisions

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9165,1.77936e-08,0.313926,0.373141,3.9017e-06,0.00321243,0.0631292,0.512982,0.649607,0.279812,0.481032,0.147402,0.278645,0.439191,0.431751,0.586217,0.012872,0.535591,0.381036,7.1833e-06,0.230489,0.653021,0.149677,0.462673,0.23568,0.213047,0.638022,0.394858,0.369527,0.207064,0.178571,0.206173,0.247225,0.48895,0.0950987,0.366377,4.33963e-07,0.183005,0.459344,0.0334302
|tfbs_overrepresentation_for_novel_motifs=0.348717,0.898711,0.341646,0.481684,0.301904,1.20684,0.554663,0.19223,0.555925,2.43082,0.450635,0.597407,0.152895,0.543352,0.81316,0.863056,0.774423,0.250594,0.163559,0.0766963,0.341703,0.047825,0.472508,0.29709,0.385586,0.619829,0.833436,0.470396,3.14801,0.388322,0.429397,0.810962,0.220667,0.154814,0.269459,2.02711,7.9481,1.20926,1.27056,0.174436,0.268162,1.06332,0.0547276,0.299183,0.949078,0.371118,0.555735,0.440085,0.0498256,0.304949,0.63387,0.567337,0.309329,0.887323,1.03948,0.546236,0.308962,0.514077,0.122557,0.513089,0.85167,0.558065,0.190442,0.746929,1.4101,0.712797,1.12756,1.49516,0.800646,1.33315,2.73679,0.573519,4.21368,1.03748,0.149081,2.6554,0.127753,2.90352,0.797419,0.989108,0.167664,0.745864,0.575394,0.19474,0.986227,2.4135,7.9978,2.45026,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,1.48306,0.239285,3.67624,0.87,0.664183,0.106284,2.76279,0.822041,0.864454,0.778061,0.701386,1.13403,0.762347,0.539961,0.385342,1.42617,0.92894,0.861701,0.893372,0.459808,1.17281,0.265019,1.199,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,1.25306,0.960022,0.432175,1.08604,0.583225,1.23359,1.20791,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,2.32574,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,2.61346,0.593875,1.14002,0.960402,0.183004,0.557588,1.36372,0.643609,0.288769,0.385642,0.357927,1.15277,0.941964,0.796636,2.5479,0.71907,0.574616,0.611402,0.553354,0.0203307
|tfbs_overrepresentation_for_novel_motifs=0.348717,0.898711,0.341646,0.481684,0.301904,1.20684,0.554663,0.19223,0.555925,2.43082,0.450635,0.597407,0.152895,0.543352,0.81316,0.863056,0.774423,0.250594,0.163559,0.0766963,0.341703,0.047825,0.472508,0.29709,0.385586,0.619829,0.833436,0.470396,3.14801,0.388322,0.429397,0.810962,0.220667,0.154814,0.269459,2.02711,7.9481,1.20926,1.27056,0.174436,0.268162,1.06332,0.0547276,0.299183,0.949078,0.371118,0.555735,0.440085,0.0498256,0.304949,0.63387,0.567337,0.309329,0.887323,1.03948,0.546236,0.308962,0.514077,0.122557,0.513089,0.85167,0.558065,0.190442,0.746929,1.4101,0.712797,1.12756,1.49516,0.800646,1.33315,2.73679,0.573519,4.21368,1.03748,0.149081,2.6554,0.127753,2.90352,0.797419,0.989108,0.167664,0.745864,0.575394,0.19474,0.986227,2.4135,7.9978,2.45026,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,1.48306,0.239285,3.67624,0.87,0.664183,0.106284,2.76279,0.822041,0.864454,0.778061,0.701386,1.13403,0.762347,0.539961,0.385342,1.42617,0.92894,0.861701,0.893372,0.459808,1.17281,0.265019,1.199,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,1.25306,0.960022,0.432175,1.08604,0.583225,1.23359,1.20791,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,2.32574,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,2.61346,0.593875,1.14002,0.960402,0.183004,0.557588,1.36372,0.643609,0.288769,0.385642,0.357927,1.15277,0.941964,0.796636,2.5479,0.71907,0.574616,0.611402,0.553354,0.0203307
|tfbs_overrepresentation_jaspar=MA0003.1;0.140538,MA0004.1;0.455723,MA0006.1;0.300178,MA0007.1;0.437331,MA0009.1;0.918715,MA0014.1;0.134069,MA0017.1;0.337901,MA0019.1;2.49556,MA0024.1;1.90464,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;5.09623,MA0050.1;1.12793,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;3.84086,MA0056.1;0,MA0057.1;1.56323,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;0.903908,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;17.2054,MA0074.1;0.552456,MA0076.1;0.377799,MA0077.1;0.880402,MA0078.1;0.652193,MA0081.1;0.361233,MA0083.1;0.926258,MA0084.1;1.42483,MA0087.1;0.885691,MA0088.1;0.770971,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;0.825856,MA0103.1;0.291333,MA0105.1;0.988431,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;0.615094,MA0144.1;0.623945,MA0145.1;0.220937,MA0146.1;0.239099,MA0147.1;0.243042,MA0148.1;0.480298,MA0149.1;2.18301,MA0062.2;0.161302,MA0035.2;0.515566,MA0039.2;1.46411,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;0.0799828,MA0155.1;0.764865,MA0156.1;0.323987,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.243637,MA0160.1;0.495355,MA0161.1;0,MA0162.1;0.0752715,MA0163.1;0.141536,MA0164.1;0.627336,MA0080.2;0.303167,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;6.80121,MA0102.2;1.46209,MA0258.1;0.209744,MA0259.1;0.699589,MA0442.1;0
}}
}}

Revision as of 19:38, 22 January 2013


Full id: C1030_Astrocyte_anaplastic_Neural_parietal_hippocampus_occipital_spinal



Phase1 CAGE Peaks

Hg19::chr14:33403589..33403617,+p@chr14:33403589..33403617
+
Hg19::chr14:33403648..33403710,+p3@NPAS3
Hg19::chr14:33403779..33403793,+p6@NPAS3
Hg19::chr14:33403860..33403874,+p5@NPAS3
Hg19::chr14:33403881..33403924,+p1@NPAS3
Hg19::chr14:33403930..33403943,+p7@NPAS3
Hg19::chr14:33705034..33705038,+p@chr14:33705034..33705038
+
Hg19::chr9:14317049..14317093,+p1@ENST00000416996


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
neural cell4.54e-1125
oligodendrocyte3.87e-087
macroglial cell3.87e-087
astrocyte3.87e-087
oligodendrocyte precursor cell3.87e-087
neuronal stem cell5.79e-078
Uber Anatomy
Ontology termp-valuen
central nervous system1.12e-7781
neural tube1.71e-7256
neural rod1.71e-7256
future spinal cord1.71e-7256
neural keel1.71e-7256
nervous system6.42e-7089
regional part of nervous system1.14e-6753
regional part of brain1.14e-6753
brain2.50e-6468
future brain2.50e-6468
neural plate5.08e-5982
presumptive neural plate5.08e-5982
neurectoderm2.39e-5786
regional part of forebrain1.68e-5341
forebrain1.68e-5341
anterior neural tube1.68e-5341
future forebrain1.68e-5341
brain grey matter4.03e-5034
gray matter4.03e-5034
telencephalon7.10e-5034
cerebral hemisphere4.38e-4732
regional part of telencephalon5.13e-4732
ecto-epithelium1.41e-45104
pre-chordal neural plate1.01e-4461
ectoderm-derived structure4.12e-42171
ectoderm4.12e-42171
presumptive ectoderm4.12e-42171
adult organism2.36e-40114
structure with developmental contribution from neural crest4.82e-37132
cerebral cortex8.46e-3725
pallium8.46e-3725
regional part of cerebral cortex8.83e-3222
neocortex1.43e-2820
organ system subdivision3.25e-28223
posterior neural tube3.24e-1915
chordal neural plate3.24e-1915
anatomical cluster3.04e-17373
segmental subdivision of hindbrain8.83e-1512
hindbrain8.83e-1512
presumptive hindbrain8.83e-1512
neural nucleus1.59e-149
nucleus of brain1.59e-149
basal ganglion1.80e-149
nuclear complex of neuraxis1.80e-149
aggregate regional part of brain1.80e-149
collection of basal ganglia1.80e-149
cerebral subcortex1.80e-149
segmental subdivision of nervous system2.09e-1313
tube2.50e-12192
epithelium3.75e-12306
cell layer7.86e-12309
telencephalic nucleus1.51e-117
organ part3.62e-11218
multi-tissue structure3.85e-11342
regional part of metencephalon1.46e-109
metencephalon1.46e-109
future metencephalon1.46e-109
brainstem3.52e-106
gyrus3.57e-106
anatomical conduit1.17e-09240
embryo1.57e-09592
limbic system3.32e-095
occipital lobe6.57e-095
developing anatomical structure7.30e-09581
temporal lobe8.95e-096
parietal lobe1.08e-085
embryonic structure1.20e-08564
germ layer1.94e-08560
germ layer / neural crest1.94e-08560
embryonic tissue1.94e-08560
presumptive structure1.94e-08560
germ layer / neural crest derived structure1.94e-08560
epiblast (generic)1.94e-08560
multi-cellular organism3.90e-08656
organ4.48e-08503
corpus striatum2.00e-074
striatum2.00e-074
ventral part of telencephalon2.00e-074
future corpus striatum2.00e-074
anatomical system5.29e-07624
anatomical group6.04e-07625
regional part of diencephalon7.40e-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)
MA0003.10.140538
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.134069
MA0017.10.337901
MA0019.12.49556
MA0024.11.90464
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
MA0048.15.09623
MA0050.11.12793
MA0051.10.553205
MA0052.10.842664
MA0055.13.84086
MA0056.10
MA0057.11.56323
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
MA0073.117.2054
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.770971
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
MA0105.10.988431
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
MA0143.10.615094
MA0144.10.623945
MA0145.10.220937
MA0146.10.239099
MA0147.10.243042
MA0148.10.480298
MA0149.12.18301
MA0062.20.161302
MA0035.20.515566
MA0039.21.46411
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
MA0154.10.0799828
MA0155.10.764865
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.0752715
MA0163.10.141536
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.26.80121
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
E2F1#186963.680541911159490.001366491550819140.0089921877056266
ZNF263#1012766.166381227758017.27120729623729e-050.00114246670499733



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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