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Coexpression cluster:C2868: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.298605,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,1.44778,0.706765,0.867962,0.341754,0.809319,0.532789,1.37557,2.39977,0.471262,0.938585,0.635753,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,0.849366,1.72987,2.28567,0.806311,0.682839,1.09415,1.10579,0.344471,0.49475,0.0842336,2.13139,0.740899,0.463978,0.971732,0.493145,0.66492,0.183156,0.53106,1.08066,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,2.64981,0.402607,0.692875,1.32819,0.893276,1.54953,0.305238,1.00941,1.08,0.62601,0.95118,1.02594,0.844168,0.399165,1.27559,2.34631,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,1.32435,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,1.28386,0.594299,1.14697,1.40954,0.717043,1.46636,0.489254,0.785429,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,2.76338,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,2.21138,2.1895,0.661255,0.437774,7.49492,0.521611,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,2.49031,1.44595,1.23002,1.07918,2.50192,0.997702,0.843324,0.423521,0.820225,5.76322
|tfbs_overrepresentation_for_novel_motifs=0.590005,0.298605,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,1.44778,0.706765,0.867962,0.341754,0.809319,0.532789,1.37557,2.39977,0.471262,0.938585,0.635753,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,0.849366,1.72987,2.28567,0.806311,0.682839,1.09415,1.10579,0.344471,0.49475,0.0842336,2.13139,0.740899,0.463978,0.971732,0.493145,0.66492,0.183156,0.53106,1.08066,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,2.64981,0.402607,0.692875,1.32819,0.893276,1.54953,0.305238,1.00941,1.08,0.62601,0.95118,1.02594,0.844168,0.399165,1.27559,2.34631,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,1.32435,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,1.28386,0.594299,1.14697,1.40954,0.717043,1.46636,0.489254,0.785429,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,2.76338,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,2.21138,2.1895,0.661255,0.437774,7.49492,0.521611,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,2.49031,1.44595,1.23002,1.07918,2.50192,0.997702,0.843324,0.423521,0.820225,5.76322
|tfbs_overrepresentation_jaspar=MA0003.1;1.45381,MA0004.1;2.8475,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;5.26462,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;5.64565,MA0050.1;2.80362,MA0051.1;3.18613,MA0052.1;1.12718,MA0055.1;2.526,MA0056.1;0,MA0057.1;0.248209,MA0058.1;1.47358,MA0059.1;1.47051,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.100363,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;1.02755,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;1.32557,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;1.29536,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;2.47057,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;1.92815,MA0145.1;6.90001,MA0146.1;0.481,MA0147.1;2.03364,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;2.51225,MA0035.2;0.778873,MA0039.2;0.0247757,MA0138.2;0.928035,MA0002.2;1.75253,MA0137.2;0.558189,MA0104.2;3.68813,MA0047.2;0.856092,MA0112.2;2.35508,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.533581,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;1.57817,MA0163.1;0.539587,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.0021048,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;3.06353,MA0442.1;0
}}
}}

Revision as of 20:58, 22 January 2013


Full id: C2868_pons_caudate_spinal_hippocampus_locus_thalamus_acute



Phase1 CAGE Peaks

Hg19::chr6:71665655..71665669,-p7@B3GAT2
Hg19::chr6:71665679..71665708,-p4@B3GAT2
Hg19::chr6:71665711..71665727,-p5@B3GAT2
Hg19::chr6:71665738..71665769,-p3@B3GAT2


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 cell3.92e-088
neural cell2.80e-0725
Uber Anatomy
Ontology termp-valuen
neural tube5.08e-8156
neural rod5.08e-8156
future spinal cord5.08e-8156
neural keel5.08e-8156
central nervous system5.08e-7981
regional part of nervous system1.27e-7453
regional part of brain1.27e-7453
nervous system2.28e-7489
brain7.94e-6568
future brain7.94e-6568
regional part of forebrain2.22e-6241
forebrain2.22e-6241
anterior neural tube2.22e-6241
future forebrain2.22e-6241
brain grey matter2.99e-5734
gray matter2.99e-5734
telencephalon9.15e-5734
neural plate6.96e-5582
presumptive neural plate6.96e-5582
regional part of telencephalon4.49e-5332
cerebral hemisphere4.57e-5332
neurectoderm1.31e-5186
ecto-epithelium1.32e-43104
pre-chordal neural plate1.67e-4261
cerebral cortex5.72e-4025
pallium5.72e-4025
regional part of cerebral cortex6.26e-3922
adult organism1.57e-35114
neocortex6.36e-3520
ectoderm-derived structure2.70e-34171
ectoderm2.70e-34171
presumptive ectoderm2.70e-34171
structure with developmental contribution from neural crest4.75e-31132
organ system subdivision4.99e-27223
posterior neural tube6.93e-1915
chordal neural plate6.93e-1915
neural nucleus1.52e-189
nucleus of brain1.52e-189
basal ganglion5.65e-189
nuclear complex of neuraxis5.65e-189
aggregate regional part of brain5.65e-189
collection of basal ganglia5.65e-189
cerebral subcortex5.65e-189
tube9.21e-16192
telencephalic nucleus1.77e-147
brainstem1.39e-136
anatomical cluster2.20e-13373
segmental subdivision of hindbrain3.42e-1312
hindbrain3.42e-1312
presumptive hindbrain3.42e-1312
gyrus2.86e-126
segmental subdivision of nervous system5.17e-1213
anatomical conduit5.61e-11240
limbic system7.82e-115
occipital lobe2.00e-105
temporal lobe2.47e-106
parietal lobe2.59e-105
corpus striatum4.70e-094
striatum4.70e-094
ventral part of telencephalon4.70e-094
future corpus striatum4.70e-094
organ part5.19e-09218
epithelium1.33e-08306
cell layer2.23e-08309
regional part of metencephalon4.41e-089
metencephalon4.41e-089
future metencephalon4.41e-089
pons7.41e-083
spinal cord7.74e-083
dorsal region element7.74e-083
dorsum7.74e-083
diencephalon1.97e-077
future diencephalon1.97e-077
medulla oblongata2.15e-073
myelencephalon2.15e-073
future myelencephalon2.15e-073
caudate-putamen2.28e-073
dorsal striatum2.28e-073
frontal cortex4.42e-073
multi-tissue structure9.23e-07342


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)
MA0003.11.45381
MA0004.12.8475
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.15.26462
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.15.64565
MA0050.12.80362
MA0051.13.18613
MA0052.11.12718
MA0055.12.526
MA0056.10
MA0057.10.248209
MA0058.11.47358
MA0059.11.47051
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.100363
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.11.32557
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.11.29536
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.12.47057
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.92815
MA0145.16.90001
MA0146.10.481
MA0147.12.03364
MA0148.10.739888
MA0149.10.769072
MA0062.22.51225
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.21.75253
MA0137.20.558189
MA0104.23.68813
MA0047.20.856092
MA0112.22.35508
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.57817
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0021048
MA0102.21.75932
MA0258.10.418966
MA0259.13.06353
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
BHLHE40#8553444.87181354697742.46312701995675e-071.28752013432064e-05
CCNT2#90546.336201576962630.0006203100587215640.00513551821029104
CTCF#1066445.360256373075030.001211145381643620.00819771954073093
CTCFL#140690419.74647435897446.5732084880439e-060.000193489098444988
E2F1#186944.907389214879320.001724022357361790.0106787955032624
E2F6#187645.017155731697390.00157802193473060.00999133269726153
EBF1#187948.9064668465690.00015887907472010.00200014123489544
EGR1#195844.988179094810140.001615011500076050.010163916002196
ELF1#199744.258097958807540.003041525565781240.0161245628713008
MAX#414946.452555509007120.0005767613195645490.00486404840552341
MYC#460945.22228187160940.001344309395272740.00889723250525281
NANOG#79923429.24477848101271.36586687657858e-065.34869781488529e-05
PAX5#507946.669565531177830.0005052774169483260.00444871591204402
RAD21#5885410.35503389545638.6948481184721e-050.00129911479634493
REST#597849.650028716128020.0001152825614219170.00157550319711379
SMC3#9126415.04493284493281.95092670935632e-050.000439596191150949
TCF7L2#6934410.77017656313737.42969445082454e-050.00115727048284812
TRIM28#10155418.59052504526258.36730015875654e-060.000230999857594601
USF1#739146.361499277207960.0006105011399140830.00508941000570617
USF2#7392412.99219738506963.50833029870167e-050.000682829869672202
YY1#752844.911170749853860.00171871838055440.0107069030090499
ZEB1#6935416.88843201754391.22862303393937e-050.000305151393677988
ZNF143#7702413.50087655222793.00867915035614e-050.000621855218254591



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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