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Coexpression cluster:C1056: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.920816,1.25141,1.62205,1.21028,0.301904,1.20684,0.554663,1.06773,0.190005,0.0394821,0.450635,0.597407,0.465048,0.543352,0.300614,0.322799,0.774423,0.250594,0.491486,0.264925,0.341703,0.180463,0.472508,0.805193,0.385586,0.619829,0.421276,0.470396,0.304828,0.777139,1.09762,0.810962,0.220667,0.469827,0.269459,1.2001,0.266487,0.481208,0.244807,0.996317,0.739305,0.413601,0.201367,0.299183,0.386203,0.371118,0.555735,0.440085,0.186577,0.822946,0.63387,0.567337,0.309329,0.887323,1.03948,0.546236,0.308962,0.514077,0.122557,0.513089,0.85167,0.558065,0.190442,0.746929,0.575742,1.69656,1.12756,1.49516,0.800646,1.33315,0.400869,0.197328,0.304852,1.03748,0.891424,0.138565,0.127753,2.90352,0.797419,0.379656,0.167664,0.745864,0.575394,4.9345,0.986227,0.450611,0.0757344,1.81046,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,0.302606,0.239285,1.51085,0.87,0.664183,0.703156,1.27523,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,0.385342,0.782066,0.352381,0.861701,0.336372,0.459808,1.17281,0.265019,0.279527,1.0951,0.710479,0.650514,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,1.35238,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,0.113443,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,0.224241,0.0833399,0.0510299,0.960402,0.183004,0.557588,1.36372,0.643609,1.433,0.385642,0.941217,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.611402,1.36282,0.446088
|tfbs_overrepresentation_jaspar=MA0003.1;0.393486,MA0004.1;0.455723,MA0006.1;0.300178,MA0007.1;0.437331,MA0009.1;0.918715,MA0014.1;0.473479,MA0017.1;0.337901,MA0019.1;0.602411,MA0024.1;0.813542,MA0025.1;1.05265,MA0027.1;2.5321,MA0028.1;0.846854,MA0029.1;0.832916,MA0030.1;0.821423,MA0031.1;0.756713,MA0038.1;1.3714,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;0.118169,MA0056.1;0,MA0057.1;2.77978,MA0058.1;0.362328,MA0059.1;0.361075,MA0060.1;1.06021,MA0061.1;0.497495,MA0063.1;0,MA0066.1;0.557833,MA0067.1;1.23721,MA0068.1;3.33244,MA0069.1;0.903908,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;0.0344109,MA0074.1;2.33338,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;1.17773,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;0.586268,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;0.673701,MA0117.1;0.956472,MA0119.1;0.913661,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;0.916926,MA0140.1;0.516266,MA0141.1;0.359385,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;0.218541,MA0145.1;0.480646,MA0146.1;1.26525,MA0147.1;0.243042,MA0148.1;1.20731,MA0149.1;0.506665,MA0062.2;0.161302,MA0035.2;0.515566,MA0039.2;0.644124,MA0138.2;1.57302,MA0002.2;1.01797,MA0137.2;0.321796,MA0104.2;1.05746,MA0047.2;0.586412,MA0112.2;0.79629,MA0065.2;0.490252,MA0150.1;0.386144,MA0151.1;0,MA0152.1;0.52279,MA0153.1;1.01778,MA0154.1;0.0799828,MA0155.1;0.43752,MA0156.1;0.865715,MA0157.1;1.66465,MA0158.1;0,MA0159.1;0.243637,MA0160.1;0.495355,MA0161.1;0,MA0162.1;0.625961,MA0163.1;0.288263,MA0164.1;0.627336,MA0080.2;0.818924,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;4.07706,MA0102.2;1.46209,MA0258.1;0.209744,MA0259.1;0.25092,MA0442.1;0
}}
}}

Revision as of 19:39, 22 January 2013


Full id: C1056_small_Neural_Astrocyte_teratocarcinoma_H9_hippocampus_testicular



Phase1 CAGE Peaks

Hg19::chr18:53019208..53019223,-p@chr18:53019208..53019223
-
Hg19::chr3:181429641..181429650,+p3@SOX2
Hg19::chr3:181429704..181429722,+p1@SOX2
Hg19::chr3:181429741..181429767,+p2@SOX2
Hg19::chr3:181431050..181431079,+p@chr3:181431050..181431079
+
Hg19::chr3:181431124..181431130,+p@chr3:181431124..181431130
+
Hg19::chr3:181431210..181431225,-p@chr3:181431210..181431225
-
Hg19::chr3:181431401..181431408,+p@chr3:181431401..181431408
+


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
central nervous system3.82e-7681
nervous system1.18e-7489
neural tube4.00e-6856
neural rod4.00e-6856
future spinal cord4.00e-6856
neural keel4.00e-6856
regional part of nervous system4.80e-6453
regional part of brain4.80e-6453
brain6.31e-6168
future brain6.31e-6168
neurectoderm4.92e-5186
regional part of forebrain1.17e-4941
forebrain1.17e-4941
anterior neural tube1.17e-4941
future forebrain1.17e-4941
neural plate5.84e-4982
presumptive neural plate5.84e-4982
ectoderm-derived structure1.04e-46171
ectoderm1.04e-46171
presumptive ectoderm1.04e-46171
brain grey matter1.67e-4234
gray matter1.67e-4234
telencephalon1.94e-4234
regional part of telencephalon5.11e-4032
cerebral hemisphere1.02e-3932
ecto-epithelium1.98e-37104
pre-chordal neural plate3.92e-3761
organ system subdivision4.18e-37223
cerebral cortex1.95e-3125
pallium1.95e-3125
structure with developmental contribution from neural crest3.04e-27132
regional part of cerebral cortex3.89e-2722
adult organism2.10e-26114
neocortex1.99e-2420
posterior neural tube8.99e-1915
chordal neural plate8.99e-1915
anatomical cluster6.02e-18373
segmental subdivision of hindbrain5.13e-1512
hindbrain5.13e-1512
presumptive hindbrain5.13e-1512
segmental subdivision of nervous system1.37e-1313
basal ganglion1.29e-129
nuclear complex of neuraxis1.29e-129
aggregate regional part of brain1.29e-129
collection of basal ganglia1.29e-129
cerebral subcortex1.29e-129
organ part1.46e-12218
neural nucleus2.38e-129
nucleus of brain2.38e-129
tube2.47e-12192
embryo1.36e-11592
regional part of metencephalon1.77e-119
metencephalon1.77e-119
future metencephalon1.77e-119
anatomical conduit4.75e-11240
telencephalic nucleus5.77e-107
germ layer1.72e-09560
germ layer / neural crest1.72e-09560
embryonic tissue1.72e-09560
presumptive structure1.72e-09560
germ layer / neural crest derived structure1.72e-09560
epiblast (generic)1.72e-09560
multi-cellular organism3.19e-09656
gyrus3.39e-096
embryonic structure3.41e-09564
developing anatomical structure9.46e-09581
brainstem1.42e-086
diencephalon1.70e-087
future diencephalon1.70e-087
multi-tissue structure3.43e-08342
limbic system3.70e-085
cerebellum4.38e-086
rhombic lip4.38e-086
temporal lobe5.56e-086
parietal lobe1.33e-075
occipital lobe3.80e-075


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)
MA0003.10.393486
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.473479
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.846854
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.11.3714
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
MA0055.10.118169
MA0056.10
MA0057.12.77978
MA0058.10.362328
MA0059.10.361075
MA0060.11.06021
MA0061.10.497495
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.13.33244
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.0344109
MA0074.12.33338
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.11.17773
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
MA0105.10.586268
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.673701
MA0117.10.956472
MA0119.10.913661
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.916926
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.480646
MA0146.11.26525
MA0147.10.243042
MA0148.11.20731
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.644124
MA0138.21.57302
MA0002.21.01797
MA0137.20.321796
MA0104.21.05746
MA0047.20.586412
MA0112.20.79629
MA0065.20.490252
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.0799828
MA0155.10.43752
MA0156.10.865715
MA0157.11.66465
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.625961
MA0163.10.288263
MA0164.10.627336
MA0080.20.818924
MA0018.20.599912
MA0099.20.523145
MA0079.24.07706
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

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

TF#promotersEnrichmentp-valueq-value
NANOG#79923414.62238924050638.55931368384764e-050.00128345464727547



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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