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Coexpression cluster:C1260: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.01633,0.0232809,0.384703,0.529489,0.343148,1.30874,0.604235,0.226729,0.224331,1.18097,1.24425,0.647852,0.541517,0.592674,3.38017,0.365029,0.827563,2.19482,1.70194,1.10853,0.384762,0.0646572,0.520063,0.338096,1.09974,0.670692,0.164928,2.22004,6.61699,0.150685,0.475674,0.864517,0.257226,0.186138,2.29455,0.021349,3.15467,0.529001,0.282922,1.7673,0.307642,0.459366,0.0729319,0.340293,1.15592,0.415364,1.47235,2.11685,0.0670664,0.346342,0.684981,0.617179,0.117127,0.941629,1.09491,0.595623,0.350547,0.562713,0.150585,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,1.13397,0.232216,0.115253,2.47482,3.87204,0.168304,0.156354,0.782748,0.850825,1.90717,0.200147,0.798651,0.625403,0.229431,1.04131,0.896187,1.62218,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,3.77603,0.343884,0.277058,1.07593,0.924148,0.715799,0.132387,0.28424,0.875714,0.918549,0.831244,0.753567,2.13786,0.815341,0.589207,2.87301,0.327379,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,10.7548,1.19482,0.762789,2.90278,1.0846,1.68811,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,1.15519,2.05191,0.345641,0.518684,1.0153,1.16378,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,2.75549,0.7715,0.624608,0.24928,0.602897,1.17335
|tfbs_overrepresentation_for_novel_motifs=1.01633,0.0232809,0.384703,0.529489,0.343148,1.30874,0.604235,0.226729,0.224331,1.18097,1.24425,0.647852,0.541517,0.592674,3.38017,0.365029,0.827563,2.19482,1.70194,1.10853,0.384762,0.0646572,0.520063,0.338096,1.09974,0.670692,0.164928,2.22004,6.61699,0.150685,0.475674,0.864517,0.257226,0.186138,2.29455,0.021349,3.15467,0.529001,0.282922,1.7673,0.307642,0.459366,0.0729319,0.340293,1.15592,0.415364,1.47235,2.11685,0.0670664,0.346342,0.684981,0.617179,0.117127,0.941629,1.09491,0.595623,0.350547,0.562713,0.150585,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,1.13397,0.232216,0.115253,2.47482,3.87204,0.168304,0.156354,0.782748,0.850825,1.90717,0.200147,0.798651,0.625403,0.229431,1.04131,0.896187,1.62218,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,3.77603,0.343884,0.277058,1.07593,0.924148,0.715799,0.132387,0.28424,0.875714,0.918549,0.831244,0.753567,2.13786,0.815341,0.589207,2.87301,0.327379,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,10.7548,1.19482,0.762789,2.90278,1.0846,1.68811,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,1.15519,2.05191,0.345641,0.518684,1.0153,1.16378,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,2.75549,0.7715,0.624608,0.24928,0.602897,1.17335
|tfbs_overrepresentation_jaspar=MA0003.1;0.358813,MA0004.1;0.502801,MA0006.1;1.62096,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;0.912418,MA0017.1;0.380797,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;0.35747,MA0029.1;0.886702,MA0030.1;0.875089,MA0031.1;0.809638,MA0038.1;0.60704,MA0040.1;0.892629,MA0041.1;0.521615,MA0042.1;0.48922,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;1.8235,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;4.89691,MA0055.1;6.55565,MA0056.1;0,MA0057.1;0.115382,MA0058.1;0.406232,MA0059.1;0.404929,MA0060.1;0.224688,MA0061.1;0.198335,MA0063.1;0,MA0066.1;0.607474,MA0067.1;2.88073,MA0068.1;0.162298,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;0.000265001,MA0074.1;0.60198,MA0076.1;0.422297,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;0.405093,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;0.538456,MA0089.1;0,MA0090.1;0.436918,MA0091.1;2.179,MA0092.1;0.467172,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.347695,MA0103.1;0.332048,MA0105.1;0.104569,MA0106.1;0.648997,MA0107.1;0.274127,MA0108.2;0.806528,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;0.269076,MA0115.1;1.21667,MA0116.1;0.277571,MA0117.1;1.01134,MA0119.1;0.388712,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,MA0130.1;0,MA0131.1;0.722072,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;0.614215,MA0139.1;0.186511,MA0140.1;0.564957,MA0141.1;0.403171,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.254954,MA0145.1;0.0807715,MA0146.1;0.324987,MA0147.1;0.281049,MA0148.1;1.30922,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;0.564239,MA0039.2;0.128723,MA0138.2;8.3919,MA0002.2;0.213296,MA0137.2;0.36398,MA0104.2;0.223944,MA0047.2;0.636643,MA0112.2;0.262665,MA0065.2;2.03906,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.102476,MA0155.1;0.071478,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;0.485816,MA0163.1;0.0167306,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;0.0109305,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;2.19656,MA0442.1;0
}}
}}

Revision as of 19:48, 22 January 2013


Full id: C1260_neuroectodermal_parietal_occipital_insula_amygdala_extraskeletal_frontal



Phase1 CAGE Peaks

Hg19::chr21:42218936..42218945,-p6@DSCAM
Hg19::chr21:42219044..42219059,-p4@DSCAM
Hg19::chr21:42219067..42219099,-p1@DSCAM
Hg19::chr21:42219120..42219129,-p10@DSCAM
Hg19::chr21:42219138..42219161,-p3@DSCAM
Hg19::chr21:42219168..42219187,-p2@DSCAM
Hg19::chr21:42219196..42219210,-p5@DSCAM


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
general ecto-epithelial cell1.20e-1114
ecto-epithelial cell4.36e-0834
Uber Anatomy
Ontology termp-valuen
neural tube8.10e-6156
neural rod8.10e-6156
future spinal cord8.10e-6156
neural keel8.10e-6156
regional part of nervous system4.61e-5653
regional part of brain4.61e-5653
central nervous system7.20e-5681
nervous system3.60e-5589
ecto-epithelium4.46e-54104
regional part of forebrain9.59e-5241
forebrain9.59e-5241
anterior neural tube9.59e-5241
future forebrain9.59e-5241
neurectoderm7.21e-4886
brain8.47e-4768
future brain8.47e-4768
neural plate1.94e-4682
presumptive neural plate1.94e-4682
telencephalon3.74e-4434
brain grey matter4.89e-4434
gray matter4.89e-4434
ectoderm-derived structure2.75e-43171
ectoderm2.75e-43171
presumptive ectoderm2.75e-43171
pre-chordal neural plate3.61e-4161
cerebral hemisphere7.31e-4132
regional part of telencephalon1.16e-4032
regional part of cerebral cortex9.78e-3822
neocortex1.42e-3420
cerebral cortex1.71e-3225
pallium1.71e-3225
structure with developmental contribution from neural crest8.50e-29132
adult organism3.21e-26114
organ system subdivision1.13e-23223
basal ganglion7.36e-139
nuclear complex of neuraxis7.36e-139
aggregate regional part of brain7.36e-139
collection of basal ganglia7.36e-139
cerebral subcortex7.36e-139
neural nucleus8.22e-139
nucleus of brain8.22e-139
organ part2.63e-12218
gyrus3.97e-126
brainstem2.76e-116
epithelium3.21e-11306
cell layer6.17e-11309
posterior neural tube1.04e-1015
chordal neural plate1.04e-1015
anatomical cluster1.80e-10373
occipital lobe1.85e-105
parietal lobe2.31e-105
temporal lobe3.79e-106
limbic system6.28e-105
telencephalic nucleus1.51e-097
tube3.51e-09192
diencephalon7.56e-097
future diencephalon7.56e-097
segmental subdivision of nervous system3.40e-0813
corpus striatum3.57e-084
striatum3.57e-084
ventral part of telencephalon3.57e-084
future corpus striatum3.57e-084
anatomical conduit1.02e-07240
organ2.03e-07503
embryonic structure6.44e-07564
segmental subdivision of hindbrain7.19e-0712
hindbrain7.19e-0712
presumptive hindbrain7.19e-0712
frontal cortex8.05e-073
pons9.36e-073


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)
MA0003.10.358813
MA0004.10.502801
MA0006.11.62096
MA0007.10.483857
MA0009.10.973289
MA0014.10.912418
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.11.8235
MA0050.10.490116
MA0051.10.602745
MA0052.14.89691
MA0055.16.55565
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.12.88073
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.000265001
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.10.436918
MA0091.12.179
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.0807715
MA0146.10.324987
MA0147.10.281049
MA0148.11.30922
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.128723
MA0138.28.3919
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.262665
MA0065.22.03906
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.071478
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.485816
MA0163.10.0167306
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.20.0109305
MA0102.21.51913
MA0258.10.245543
MA0259.12.19656
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
REST#597879.650028716128021.28195528172884e-077.32418641512461e-06
SUZ12#23512750.11578091106291.25242994278099e-121.74636222689057e-10
TBP#690873.706770687096390.0001039672097505110.00145182931128943
USF1#739176.361499277207962.37038582734158e-068.40613668664607e-05



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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