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Coexpression cluster:C2264: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.44014,2.11192,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.902371,2.82941,0.867962,0.341754,0.809319,0.532789,0.559384,2.39977,0.471262,0.356737,1.18986,0.581762,0.169357,0.731221,0.528529,2.59358,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,2.67722,2.13139,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,0.314427,1.49501,1.92371,1.65941,0.515703,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,0.393426,2.3411,1.96835,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,7.68497,1.32819,1.6033,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,2.33882,0.844168,0.399165,1.27559,0.353274,0.221873,0.291738,5.05541,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,2.16273,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,4.0753,1.04326,0.805616,1.52945,1.28386,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,1.85914,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,2.52313,1.36323,3.00169,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,7.15009,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,1.58937,0.437774,0.234974,18.0146,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,1.47036,0.997702,1.96584,0.423521,0.820225,0.0401987
|tfbs_overrepresentation_for_novel_motifs=1.44014,2.11192,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.902371,2.82941,0.867962,0.341754,0.809319,0.532789,0.559384,2.39977,0.471262,0.356737,1.18986,0.581762,0.169357,0.731221,0.528529,2.59358,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,2.67722,2.13139,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,0.314427,1.49501,1.92371,1.65941,0.515703,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,0.393426,2.3411,1.96835,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,7.68497,1.32819,1.6033,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,2.33882,0.844168,0.399165,1.27559,0.353274,0.221873,0.291738,5.05541,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,2.16273,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,4.0753,1.04326,0.805616,1.52945,1.28386,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,1.85914,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,2.52313,1.36323,3.00169,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,7.15009,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,1.58937,0.437774,0.234974,18.0146,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,1.47036,0.997702,1.96584,0.423521,0.820225,0.0401987
|tfbs_overrepresentation_jaspar=MA0003.1;0.443649,MA0004.1;0.71247,MA0006.1;2.26728,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;1.34758,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;1.35734,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;0.709734,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.791759,MA0056.1;0,MA0057.1;4.57701,MA0058.1;0.605914,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;0.214613,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;1.62583,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;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;2.17614,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;1.63368,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;0.061409,MA0147.1;1.16748,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.931615,MA0035.2;0.778873,MA0039.2;1.13403,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;1.01696,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;0.577908,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;1.61785,MA0156.1;1.37856,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;2.80246,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;4.91669,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;3.06353,MA0442.1;0
}}
}}

Revision as of 20:31, 22 January 2013


Full id: C2264_occipital_parietal_pineal_temporal_duodenum_brain_optic



Phase1 CAGE Peaks

Hg19::chr13:44361004..44361022,-p3@ENOX1
Hg19::chr13:44361025..44361052,-p1@ENOX1
Hg19::chr13:44361058..44361095,-p2@ENOX1
Hg19::chr13:44361100..44361121,-p4@ENOX1


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
fibroblast2.18e-0976
muscle precursor cell1.61e-0758
myoblast1.61e-0758
multi-potent skeletal muscle stem cell1.61e-0758
muscle cell2.17e-0755
electrically responsive cell2.93e-0761
electrically active cell2.93e-0761
Uber Anatomy
Ontology termp-valuen
nervous system7.22e-2789
neural tube1.50e-2656
neural rod1.50e-2656
future spinal cord1.50e-2656
neural keel1.50e-2656
structure with developmental contribution from neural crest1.46e-25132
central nervous system4.95e-2581
regional part of nervous system6.53e-2553
regional part of brain6.53e-2553
neural plate3.89e-2382
presumptive neural plate3.89e-2382
brain5.66e-2368
future brain5.66e-2368
regional part of forebrain3.56e-2241
forebrain3.56e-2241
anterior neural tube3.56e-2241
future forebrain3.56e-2241
multi-tissue structure5.75e-22342
ectoderm-derived structure2.89e-21171
ectoderm2.89e-21171
presumptive ectoderm2.89e-21171
neurectoderm8.32e-2186
ecto-epithelium8.99e-21104
adult organism2.22e-20114
organ system subdivision2.53e-20223
anatomical cluster5.33e-20373
cell layer3.09e-19309
epithelium5.31e-19306
telencephalon5.51e-1934
brain grey matter6.18e-1934
gray matter6.18e-1934
regional part of telencephalon1.06e-1732
cerebral hemisphere1.07e-1732
pre-chordal neural plate1.26e-1661
regional part of cerebral cortex3.23e-1422
tube4.01e-14192
multi-cellular organism1.01e-13656
cerebral cortex1.85e-1325
pallium1.85e-1325
anatomical system3.20e-13624
neocortex3.29e-1320
anatomical group5.92e-13625
embryonic structure1.57e-12564
germ layer1.57e-12560
germ layer / neural crest1.57e-12560
embryonic tissue1.57e-12560
presumptive structure1.57e-12560
germ layer / neural crest derived structure1.57e-12560
epiblast (generic)1.57e-12560
anatomical conduit2.87e-12240
embryo1.17e-10592
dense mesenchyme tissue2.56e-1073
developing anatomical structure3.18e-10581
paraxial mesoderm5.72e-1072
presumptive paraxial mesoderm5.72e-1072
organ part1.04e-09218
somite1.58e-0971
presomitic mesoderm1.58e-0971
presumptive segmental plate1.58e-0971
dermomyotome1.58e-0971
trunk paraxial mesoderm1.58e-0971
muscle tissue3.12e-0964
musculature3.12e-0964
musculature of body3.12e-0964
skeletal muscle tissue7.56e-0962
striated muscle tissue7.56e-0962
myotome7.56e-0962
multilaminar epithelium1.14e-0783
tissue2.99e-07773
organ3.51e-07503
neural nucleus5.14e-079
nucleus of brain5.14e-079
basal ganglion7.36e-079
nuclear complex of neuraxis7.36e-079
aggregate regional part of brain7.36e-079
collection of basal ganglia7.36e-079
cerebral subcortex7.36e-079
epithelial vesicle7.61e-0778


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
MA0006.12.26728
MA0007.10.6918
MA0009.11.20602
MA0014.11.34758
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.14.57701
MA0058.10.605914
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
MA0073.10.214613
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.62583
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
MA0105.10.232357
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
MA0131.12.17614
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.11.63368
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.21.13403
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.187982
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.61785
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.12.80246
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.24.91669
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
CTCF#1066445.360256373075030.001211145381643620.00816227737713611
E2F1#186944.907389214879320.001724022357361790.0106321329188372
RAD21#5885410.35503389545638.6948481184721e-050.00129153924426839
REST#597849.650028716128020.0001152825614219170.00156832036372849



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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