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Coexpression cluster:C2494: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,1.03954,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,1.01802,1.44778,0.706765,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.635753,0.581762,0.505745,1.73475,0.528529,0.632849,0.892087,0.849366,0.728867,0.537869,0.806311,0.682839,1.09415,1.93746,0.911389,0.49475,10.1969,0.491074,0.740899,0.463978,4.60518,0.493145,0.66492,0.183156,0.53106,1.08066,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.692875,1.32819,0.336329,0.859396,0.823598,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,3.99585,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,2.59267,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.393155,0.681522,0.988625,1.1313,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,1.15964,1.24863,0.68598,1.37788,0.852645,1.52813,1.41398,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.644569
|tfbs_overrepresentation_for_novel_motifs=0.590005,1.03954,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,1.01802,1.44778,0.706765,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.635753,0.581762,0.505745,1.73475,0.528529,0.632849,0.892087,0.849366,0.728867,0.537869,0.806311,0.682839,1.09415,1.93746,0.911389,0.49475,10.1969,0.491074,0.740899,0.463978,4.60518,0.493145,0.66492,0.183156,0.53106,1.08066,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.692875,1.32819,0.336329,0.859396,0.823598,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,3.99585,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,2.59267,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.393155,0.681522,0.988625,1.1313,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,1.15964,1.24863,0.68598,1.37788,0.852645,1.52813,1.41398,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.644569
|tfbs_overrepresentation_jaspar=MA0003.1;0.443649,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.524262,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;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;1.8712,MA0056.1;0,MA0057.1;1.98521,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;1.52107,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;5.01475,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;0.536981,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;1.90157,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;0.344952,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.221129,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;3.07509,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;2.43626,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.649108,MA0155.1;1.61785,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.309472,MA0163.1;1.37853,MA0164.1;0.90014,MA0080.2;1.32578,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;16.1395,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:42, 22 January 2013


Full id: C2494_brain_neuroblastoma_duodenum_occipital_temporal_parietal_small



Phase1 CAGE Peaks

Hg19::chr19:4474846..4474881,+p@chr19:4474846..4474881
+
Hg19::chr20:42875935..42875966,+p1@GDAP1L1
Hg19::chr6:3228944..3228955,+p2@uc003mvi.1
Hg19::chr6:33388013..33388053,+p4@SYNGAP1


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
nervous system1.17e-5789
central nervous system8.00e-5581
neurectoderm2.68e-4686
neural tube1.02e-4556
neural rod1.02e-4556
future spinal cord1.02e-4556
neural keel1.02e-4556
neural plate2.62e-4582
presumptive neural plate2.62e-4582
regional part of nervous system2.35e-4353
regional part of brain2.35e-4353
brain6.38e-4368
future brain6.38e-4368
ectoderm-derived structure5.52e-41171
ectoderm5.52e-41171
presumptive ectoderm5.52e-41171
pre-chordal neural plate1.20e-3561
regional part of forebrain2.19e-3441
forebrain2.19e-3441
anterior neural tube2.19e-3441
future forebrain2.19e-3441
ecto-epithelium4.42e-34104
structure with developmental contribution from neural crest9.43e-31132
telencephalon1.23e-2934
brain grey matter1.86e-2934
gray matter1.86e-2934
cerebral hemisphere1.96e-2832
regional part of telencephalon5.36e-2832
organ system subdivision3.83e-27223
cerebral cortex5.28e-2325
pallium5.28e-2325
regional part of cerebral cortex3.34e-2122
neocortex1.88e-1920
adult organism1.97e-19114
anatomical cluster8.86e-18373
multi-tissue structure1.80e-12342
posterior neural tube3.70e-1215
chordal neural plate3.70e-1215
organ part3.17e-11218
segmental subdivision of hindbrain5.53e-1012
hindbrain5.53e-1012
presumptive hindbrain5.53e-1012
embryo9.58e-10592
segmental subdivision of nervous system6.96e-0913
epithelium1.17e-08306
cell layer2.77e-08309
basal ganglion3.15e-089
nuclear complex of neuraxis3.15e-089
aggregate regional part of brain3.15e-089
collection of basal ganglia3.15e-089
cerebral subcortex3.15e-089
multi-cellular organism3.95e-08656
neural nucleus6.93e-089
nucleus of brain6.93e-089
regional part of metencephalon7.76e-089
metencephalon7.76e-089
future metencephalon7.76e-089
developing anatomical structure7.89e-08581
tube1.02e-07192
germ layer1.36e-07560
germ layer / neural crest1.36e-07560
embryonic tissue1.36e-07560
presumptive structure1.36e-07560
germ layer / neural crest derived structure1.36e-07560
epiblast (generic)1.36e-07560
embryonic structure1.53e-07564
temporal lobe1.66e-076


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)
MA0003.10.443649
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
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
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.11.8712
MA0056.10
MA0057.11.98521
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.11.52107
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.15.01475
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.11.90157
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
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.23.07509
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.22.43626
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.11.61785
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.11.37853
MA0164.10.90014
MA0080.21.32578
MA0018.20.870662
MA0099.20.7872
MA0079.216.1395
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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

No analysis results for this cluster

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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