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Coexpression cluster:C1015: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.348717,0.0704539,1.62205,0.481684,0.301904,1.20684,0.554663,0.19223,0.555925,3.01148,1.99636,0.597407,0.152895,0.543352,0.300614,0.322799,0.774423,0.250594,0.163559,0.264925,0.341703,0.180463,0.472508,0.29709,0.385586,0.619829,0.135503,0.470396,0.304828,1.26774,1.09762,0.810962,0.220667,0.469827,0.269459,3.0201,0.266487,0.481208,0.685417,0.174436,0.268162,1.06332,0.201367,0.299183,3.23731,0.371118,2.34408,0.440085,0.186577,0.822946,0.63387,0.567337,0.639783,0.887323,1.03948,1.34776,0.308962,0.514077,0.122557,0.513089,0.85167,0.558065,0.190442,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.197328,0.0911419,1.03748,0.455523,0.429044,0.401476,0.730167,0.797419,0.379656,0.167664,0.745864,0.575394,0.19474,0.986227,1.47034,0.0757344,3.91012,0.659621,1.59442,1.22073,0.959334,3.20987,0.227232,0.302606,0.672575,0.162291,0.87,0.664183,1.70117,0.246049,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,0.385342,0.286892,0.352381,0.861701,0.336372,3.00947,1.17281,0.732093,0.518187,0.428232,0.710479,0.229841,1.02923,2.67165,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,1.42587,1.23359,1.20791,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,2.32574,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,1.85818,0.0833399,0.0510299,0.960402,1.03091,2.35012,1.36372,0.643609,0.288769,0.385642,1.67913,1.15277,0.941964,0.796636,0.36101,0.71907,1.40773,0.213234,0.553354,1.23035
|tfbs_overrepresentation_for_novel_motifs=0.348717,0.0704539,1.62205,0.481684,0.301904,1.20684,0.554663,0.19223,0.555925,3.01148,1.99636,0.597407,0.152895,0.543352,0.300614,0.322799,0.774423,0.250594,0.163559,0.264925,0.341703,0.180463,0.472508,0.29709,0.385586,0.619829,0.135503,0.470396,0.304828,1.26774,1.09762,0.810962,0.220667,0.469827,0.269459,3.0201,0.266487,0.481208,0.685417,0.174436,0.268162,1.06332,0.201367,0.299183,3.23731,0.371118,2.34408,0.440085,0.186577,0.822946,0.63387,0.567337,0.639783,0.887323,1.03948,1.34776,0.308962,0.514077,0.122557,0.513089,0.85167,0.558065,0.190442,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.197328,0.0911419,1.03748,0.455523,0.429044,0.401476,0.730167,0.797419,0.379656,0.167664,0.745864,0.575394,0.19474,0.986227,1.47034,0.0757344,3.91012,0.659621,1.59442,1.22073,0.959334,3.20987,0.227232,0.302606,0.672575,0.162291,0.87,0.664183,1.70117,0.246049,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,0.385342,0.286892,0.352381,0.861701,0.336372,3.00947,1.17281,0.732093,0.518187,0.428232,0.710479,0.229841,1.02923,2.67165,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,1.42587,1.23359,1.20791,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,2.32574,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,1.85818,0.0833399,0.0510299,0.960402,1.03091,2.35012,1.36372,0.643609,0.288769,0.385642,1.67913,1.15277,0.941964,0.796636,0.36101,0.71907,1.40773,0.213234,0.553354,1.23035
|tfbs_overrepresentation_jaspar=MA0003.1;0.797136,MA0004.1;0.455723,MA0006.1;0.812175,MA0007.1;0.437331,MA0009.1;0.918715,MA0014.1;1.78293,MA0017.1;0.896777,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;0.316923,MA0050.1;0.443405,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;0.028436,MA0056.1;0,MA0057.1;1.56323,MA0058.1;0.362328,MA0059.1;0.361075,MA0060.1;0.190336,MA0061.1;0.961853,MA0063.1;0,MA0066.1;0.557833,MA0067.1;1.23721,MA0068.1;0.823119,MA0069.1;0.903908,MA0070.1;0.892666,MA0071.1;1.28975,MA0072.1;0.888148,MA0073.1;0.0041831,MA0074.1;0.552456,MA0076.1;0.377799,MA0077.1;2.04187,MA0078.1;3.86188,MA0081.1;0.361233,MA0083.1;0.926258,MA0084.1;1.42483,MA0087.1;0.885691,MA0088.1;3.41003,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;4.79011,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;0.345493,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;0.916926,MA0140.1;0.516266,MA0141.1;0.359385,MA0142.1;0.724856,MA0143.1;1.49284,MA0144.1;0.218541,MA0145.1;0.0613434,MA0146.1;0.239099,MA0147.1;0.243042,MA0148.1;0.480298,MA0149.1;0.506665,MA0062.2;0.161302,MA0035.2;0.515566,MA0039.2;4.9691,MA0138.2;0.653421,MA0002.2;0.179788,MA0137.2;0.321796,MA0104.2;0.189646,MA0047.2;0.586412,MA0112.2;0.458158,MA0065.2;0.0631316,MA0150.1;0.386144,MA0151.1;0,MA0152.1;0.52279,MA0153.1;1.01778,MA0154.1;2.00298,MA0155.1;0.197713,MA0156.1;0.323987,MA0157.1;0.697424,MA0158.1;0,MA0159.1;2.74647,MA0160.1;0.495355,MA0161.1;0,MA0162.1;0.0752715,MA0163.1;5.02939,MA0164.1;0.627336,MA0080.2;0.303167,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;15.4497,MA0102.2;1.46209,MA0258.1;0.209744,MA0259.1;0.25092,MA0442.1;0
}}
}}

Revision as of 19:37, 22 January 2013


Full id: C1015_occipital_neuroectodermal_temporal_parietal_duodenum_brain_small



Phase1 CAGE Peaks

Hg19::chr12:45269119..45269133,-p@chr12:45269119..45269133
-
Hg19::chr12:45269871..45269882,-p5@NELL2
Hg19::chr12:45269952..45269963,-p6@NELL2
Hg19::chr12:45269964..45269979,-p2@NELL2
Hg19::chr12:45269990..45270001,-p4@NELL2
Hg19::chr12:45270077..45270143,-p1@NELL2
Hg19::chr12:45270151..45270162,-p3@NELL2
Hg19::chr17:44091602..44091622,+p@chr17:44091602..44091622
+


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>disease_data<br>

Cell Type
Ontology termp-valuen
mature alpha-beta T cell1.72e-1318
alpha-beta T cell1.72e-1318
immature T cell1.72e-1318
mature T cell1.72e-1318
immature alpha-beta T cell1.72e-1318
CD8-positive, alpha-beta T cell3.89e-1311
T cell2.18e-0825
pro-T cell2.18e-0825
neuron2.02e-076
neuroblast2.02e-076
electrically signaling cell2.02e-076
neuronal stem cell3.50e-078
Uber Anatomy
Ontology termp-valuen
nervous system1.56e-4389
central nervous system1.85e-4381
neural tube3.78e-4256
neural rod3.78e-4256
future spinal cord3.78e-4256
neural keel3.78e-4256
regional part of nervous system1.82e-4153
regional part of brain1.82e-4153
adult organism6.64e-39114
neurectoderm7.00e-3886
regional part of forebrain4.90e-3541
forebrain4.90e-3541
anterior neural tube4.90e-3541
future forebrain4.90e-3541
brain6.31e-3568
future brain6.31e-3568
neural plate1.81e-3482
presumptive neural plate1.81e-3482
pre-chordal neural plate4.72e-3161
cerebral hemisphere3.14e-2932
telencephalon6.89e-2934
regional part of cerebral cortex1.21e-2822
brain grey matter2.06e-2834
gray matter2.06e-2834
regional part of telencephalon7.98e-2732
neocortex2.78e-2620
ecto-epithelium2.11e-25104
ectoderm-derived structure2.15e-25171
ectoderm2.15e-25171
presumptive ectoderm2.15e-25171
cerebral cortex2.80e-2425
pallium2.80e-2425
organ system subdivision1.25e-19223
structure with developmental contribution from neural crest1.24e-16132
temporal lobe1.89e-096
anatomical cluster2.89e-09373
gyrus1.02e-086
posterior neural tube1.63e-0815
chordal neural plate1.63e-0815
segmental subdivision of hindbrain9.37e-0812
hindbrain9.37e-0812
presumptive hindbrain9.37e-0812
parietal lobe1.20e-075
occipital lobe1.39e-075
diencephalon1.67e-077
future diencephalon1.67e-077
limbic system2.19e-075
segmental subdivision of nervous system5.65e-0713
brainstem9.15e-076
Disease
Ontology termp-valuen
neuroectodermal tumor8.81e-0710


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)
MA0003.10.797136
MA0004.10.455723
MA0006.10.812175
MA0007.10.437331
MA0009.10.918715
MA0014.11.78293
MA0017.10.896777
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
MA0048.10.316923
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.028436
MA0056.10
MA0057.11.56323
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.961853
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.823119
MA0069.10.903908
MA0070.10.892666
MA0071.11.28975
MA0072.10.888148
MA0073.10.0041831
MA0074.10.552456
MA0076.10.377799
MA0077.12.04187
MA0078.13.86188
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.13.41003
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
MA0105.14.79011
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
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.916926
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.11.49284
MA0144.10.218541
MA0145.10.0613434
MA0146.10.239099
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.24.9691
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.458158
MA0065.20.0631316
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.12.00298
MA0155.10.197713
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.12.74647
MA0160.10.495355
MA0161.10
MA0162.10.0752715
MA0163.15.02939
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.215.4497
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
CTBP2#1488215.6792500848320.006675872541887170.0284046872159274



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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