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Coexpression cluster:C1058: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.348717,1.6536,0.341646,0.481684,0.301904,0.480078,0.554663,0.19223,1.05889,1.89747,1.99636,0.597407,0.907465,2.30362,0.300614,0.863056,0.774423,0.250594,0.163559,0.0766963,0.341703,0.405031,0.472508,0.29709,0.385586,0.619829,0.833436,0.470396,0.304828,0.777139,0.429397,0.810962,0.220667,0.469827,0.269459,1.2001,0.266487,0.481208,0.244807,0.174436,0.268162,0.413601,0.0547276,0.299183,0.637759,0.371118,0.555735,1.12076,0.416595,0.304949,0.63387,1.39237,0.0927889,0.887323,1.03948,0.546236,0.308962,0.514077,0.388089,1.27736,0.85167,0.558065,0.190442,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,1.82757,0.197328,2.77815,1.03748,0.149081,0.138565,0.127753,0.730167,0.797419,0.379656,0.167664,0.745864,1.40937,0.19474,0.986227,1.47034,0.9432,1.81046,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,4.08104,0.239285,0.162291,0.87,0.664183,1.70117,0.246049,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,3.64597,0.286892,0.352381,0.861701,0.336372,0.459808,1.17281,0.732093,0.518187,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,2.44413,1.28328,0.730921,0.548418,1.94386,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,0.735874,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,1.1925,0.593875,2.70449,0.960402,3.08046,0.557588,1.36372,0.643609,0.288769,0.385642,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.213234,0.553354,0.664626
|tfbs_overrepresentation_for_novel_motifs=0.348717,1.6536,0.341646,0.481684,0.301904,0.480078,0.554663,0.19223,1.05889,1.89747,1.99636,0.597407,0.907465,2.30362,0.300614,0.863056,0.774423,0.250594,0.163559,0.0766963,0.341703,0.405031,0.472508,0.29709,0.385586,0.619829,0.833436,0.470396,0.304828,0.777139,0.429397,0.810962,0.220667,0.469827,0.269459,1.2001,0.266487,0.481208,0.244807,0.174436,0.268162,0.413601,0.0547276,0.299183,0.637759,0.371118,0.555735,1.12076,0.416595,0.304949,0.63387,1.39237,0.0927889,0.887323,1.03948,0.546236,0.308962,0.514077,0.388089,1.27736,0.85167,0.558065,0.190442,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,1.82757,0.197328,2.77815,1.03748,0.149081,0.138565,0.127753,0.730167,0.797419,0.379656,0.167664,0.745864,1.40937,0.19474,0.986227,1.47034,0.9432,1.81046,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,4.08104,0.239285,0.162291,0.87,0.664183,1.70117,0.246049,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,3.64597,0.286892,0.352381,0.861701,0.336372,0.459808,1.17281,0.732093,0.518187,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,2.44413,1.28328,0.730921,0.548418,1.94386,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,0.735874,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,1.1925,0.593875,2.70449,0.960402,3.08046,0.557588,1.36372,0.643609,0.288769,0.385642,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.213234,0.553354,0.664626
|tfbs_overrepresentation_jaspar=MA0003.1;0.576745,MA0004.1;0.455723,MA0006.1;3.11831,MA0007.1;0.437331,MA0009.1;0.918715,MA0014.1;2.22106,MA0017.1;0.337901,MA0019.1;2.49556,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;0.653157,MA0050.1;0.443405,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;0.028436,MA0056.1;0,MA0057.1;13.5716,MA0058.1;0.362328,MA0059.1;0.361075,MA0060.1;0.190336,MA0061.1;0.497495,MA0063.1;0,MA0066.1;0.557833,MA0067.1;1.23721,MA0068.1;0.415214,MA0069.1;0.903908,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;4.5734,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;1.6523,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;1.47197,MA0106.1;0.59853,MA0107.1;1.23931,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;1.60834,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;0.218541,MA0145.1;0.0613434,MA0146.1;0.0399277,MA0147.1;0.681318,MA0148.1;0.480298,MA0149.1;3.22166,MA0062.2;0.161302,MA0035.2;0.515566,MA0039.2;1.80526,MA0138.2;0.653421,MA0002.2;0.179788,MA0137.2;0.321796,MA0104.2;0.55506,MA0047.2;0.586412,MA0112.2;0.208783,MA0065.2;1.78056,MA0150.1;0.386144,MA0151.1;0,MA0152.1;0.52279,MA0153.1;1.01778,MA0154.1;0.0799828,MA0155.1;0.197713,MA0156.1;0.323987,MA0157.1;0.697424,MA0158.1;0,MA0159.1;3.60701,MA0160.1;0.495355,MA0161.1;0,MA0162.1;0.625961,MA0163.1;0.288263,MA0164.1;0.627336,MA0080.2;0.303167,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;16.0339,MA0102.2;1.46209,MA0258.1;0.209744,MA0259.1;0.699589,MA0442.1;0
}}
}}

Revision as of 19:39, 22 January 2013


Full id: C1058_cerebellum_parietal_occipital_pineal_brain_retinoblastoma_temporal



Phase1 CAGE Peaks

Hg19::chr19:10515584..10515599,+p@chr19:10515584..10515599
+
Hg19::chr1:57889966..57889983,-p6@DAB1
Hg19::chr8:9760906..9760907,-p1@ENST00000517675
Hg19::chr8:9763201..9763208,-p7@ENST00000521242
Hg19::chr8:9763221..9763232,-p4@ENST00000521242
Hg19::chr8:9763242..9763268,-p1@ENST00000521242
Hg19::chr8:9763271..9763300,-p3@ENST00000521242
Hg19::chr8:9763301..9763343,-p2@ENST00000521242


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
neuronal stem cell8.08e-128
neuron1.14e-116
neuroblast1.14e-116
electrically signaling cell1.14e-116
embryonic stem cell7.96e-095
Uber Anatomy
Ontology termp-valuen
central nervous system9.89e-8181
nervous system1.20e-7889
neural tube1.20e-7156
neural rod1.20e-7156
future spinal cord1.20e-7156
neural keel1.20e-7156
regional part of nervous system1.67e-6653
regional part of brain1.67e-6653
brain1.74e-6168
future brain1.74e-6168
regional part of forebrain1.99e-5441
forebrain1.99e-5441
anterior neural tube1.99e-5441
future forebrain1.99e-5441
neural plate2.73e-5182
presumptive neural plate2.73e-5182
neurectoderm3.32e-5086
cerebral hemisphere1.40e-4832
brain grey matter1.91e-4834
gray matter1.91e-4834
telencephalon2.16e-4834
regional part of telencephalon5.74e-4532
regional part of cerebral cortex1.08e-4122
pre-chordal neural plate6.44e-4061
neocortex7.33e-3820
ecto-epithelium2.74e-37104
ectoderm-derived structure1.18e-36171
ectoderm1.18e-36171
presumptive ectoderm1.18e-36171
cerebral cortex4.87e-3625
pallium4.87e-3625
adult organism8.14e-31114
structure with developmental contribution from neural crest3.32e-30132
organ system subdivision4.53e-27223
posterior neural tube1.46e-1715
chordal neural plate1.46e-1715
tube2.46e-14192
basal ganglion7.27e-149
nuclear complex of neuraxis7.27e-149
aggregate regional part of brain7.27e-149
collection of basal ganglia7.27e-149
cerebral subcortex7.27e-149
neural nucleus1.27e-139
nucleus of brain1.27e-139
gyrus3.14e-136
segmental subdivision of hindbrain6.58e-1312
hindbrain6.58e-1312
presumptive hindbrain6.58e-1312
anatomical cluster2.64e-12373
segmental subdivision of nervous system9.32e-1213
brainstem1.23e-116
parietal lobe1.79e-115
occipital lobe4.30e-115
temporal lobe5.33e-116
limbic system5.40e-115
telencephalic nucleus2.80e-107
regional part of diencephalon2.88e-094
corpus striatum5.57e-094
striatum5.57e-094
ventral part of telencephalon5.57e-094
future corpus striatum5.57e-094
anatomical conduit7.29e-09240
regional part of metencephalon1.94e-089
metencephalon1.94e-089
future metencephalon1.94e-089
organ part8.80e-08218
diencephalon1.49e-077
future diencephalon1.49e-077
frontal cortex1.76e-073
caudate-putamen4.31e-073
dorsal striatum4.31e-073
pons7.93e-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)
MA0003.10.576745
MA0004.10.455723
MA0006.13.11831
MA0007.10.437331
MA0009.10.918715
MA0014.12.22106
MA0017.10.337901
MA0019.12.49556
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
MA0048.10.653157
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.028436
MA0056.10
MA0057.113.5716
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.497495
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.415214
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.14.5734
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.11.6523
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
MA0105.11.47197
MA0106.10.59853
MA0107.11.23931
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
MA0131.11.60834
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
MA0144.10.218541
MA0145.10.0613434
MA0146.10.0399277
MA0147.10.681318
MA0148.10.480298
MA0149.13.22166
MA0062.20.161302
MA0035.20.515566
MA0039.21.80526
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.55506
MA0047.20.586412
MA0112.20.208783
MA0065.21.78056
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.0799828
MA0155.10.197713
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.13.60701
MA0160.10.495355
MA0161.10
MA0162.10.625961
MA0163.10.288263
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.216.0339
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
SUZ12#23512531.32236306941431.68017316924325e-079.26481550277698e-06



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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