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Coexpression cluster:C1242: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.392069,0.247072,0.384703,0.529489,0.343148,0.52784,1.47005,0.226729,0.224331,0.443077,0.497563,0.647852,0.541517,0.592674,0.341795,0.365029,0.827563,0.28906,0.19568,0.0986842,0.384762,0.0646572,0.520063,0.338096,2.87418,0.670692,0.164928,0.517892,0.915262,0.150685,0.475674,0.864517,0.257226,0.546594,0.309012,1.45077,0.305874,0.529001,0.282922,1.12779,0.307642,1.16235,0.0729319,0.340293,0.494995,0.415364,0.60533,0.486696,0.0670664,0.915545,0.684981,1.49721,0.752493,0.941629,1.09491,0.595623,0.350547,0.562713,0.459282,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,0.369103,1.0929,0.179863,0.503161,0.156354,0.782748,0.850825,0.424224,0.200147,0.798651,0.625403,0.229431,1.04131,0.896187,0.097572,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.277058,1.69423,0.924148,0.715799,0.413337,0.28424,0.875714,0.918549,0.831244,0.753567,1.23455,0.815341,0.589207,0.43012,0.327379,0.395884,0.915771,0.379203,0.507004,1.22894,0.821533,0.642446,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,2.05416,1.12733,1.39367,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.26104,0.106334,0.241704,1.0153,0.216774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,1.28735,0.602897,0.0992692
|tfbs_overrepresentation_jaspar=MA0003.1;0.213534,MA0004.1;0.502801,MA0006.1;1.62096,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;0.367415,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;0.766755,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;0.0407081,MA0056.1;0,MA0057.1;1.22064,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;1.29359,MA0068.1;7.33233,MA0069.1;0.958358,MA0070.1;3.58082,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;82.2519,MA0074.1;1.46532,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;0.917255,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,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;0.340955,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;3.88344,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;2.82265,MA0145.1;0.0807715,MA0146.1;0.828373,MA0147.1;0.281049,MA0148.1;0.528066,MA0149.1;5.89542,MA0062.2;0.193221,MA0035.2;0.564239,MA0039.2;3.59026,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;1.70023,MA0104.2;0.223944,MA0047.2;0.636643,MA0112.2;0.262665,MA0065.2;0.591589,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;2.27082,MA0155.1;0.250175,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;4.30675,MA0163.1;5.04376,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;26.7981,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;0.289405,MA0442.1;0
}}
}}

Revision as of 19:47, 22 January 2013


Full id: C1242_Mast_anaplastic_putamen_caudate_nucleus_occipital_insula



Phase1 CAGE Peaks

Hg19::chr19:47105424..47105433,+p32@CALM3
Hg19::chr3:171178035..171178046,-p7@TNIK
Hg19::chr3:71181437..71181451,-p@chr3:71181437..71181451
-
Hg19::chr8:22550045..22550063,-p8@EGR3
Hg19::chr8:22550509..22550526,-p6@EGR3
Hg19::chr8:22550530..22550609,-p2@EGR3
Hg19::chr8:22550700..22550717,-p4@EGR3


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

GO IDGO nameFDR corrected p-value
GO:0007274neuromuscular synaptic transmission0.0445020006415389
GO:0007422peripheral nervous system development0.0477843731091476
GO:0007623circadian rhythm0.0477843731091476



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
telencephalon9.04e-8534
cerebral hemisphere1.12e-8432
regional part of forebrain4.48e-7941
forebrain4.48e-7941
anterior neural tube4.48e-7941
future forebrain4.48e-7941
regional part of telencephalon1.18e-7832
brain grey matter1.02e-7334
gray matter1.02e-7334
regional part of cerebral cortex3.83e-7022
regional part of nervous system2.89e-6753
regional part of brain2.89e-6753
neocortex1.31e-6320
neural tube2.98e-6356
neural rod2.98e-6356
future spinal cord2.98e-6356
neural keel2.98e-6356
cerebral cortex2.39e-6125
pallium2.39e-6125
brain3.24e-5368
future brain3.24e-5368
pre-chordal neural plate8.47e-5161
central nervous system5.24e-4981
nervous system7.83e-4689
neural plate1.24e-4082
presumptive neural plate1.24e-4082
neurectoderm2.34e-3886
adult organism7.79e-35114
ecto-epithelium2.36e-32104
structure with developmental contribution from neural crest1.31e-28132
basal ganglion1.27e-249
nuclear complex of neuraxis1.27e-249
aggregate regional part of brain1.27e-249
collection of basal ganglia1.27e-249
cerebral subcortex1.27e-249
ectoderm-derived structure2.04e-22171
ectoderm2.04e-22171
presumptive ectoderm2.04e-22171
gyrus1.31e-216
organ system subdivision3.06e-19223
telencephalic nucleus2.42e-187
parietal lobe3.96e-185
temporal lobe5.73e-186
limbic system5.81e-185
occipital lobe1.20e-175
tube1.16e-15192
corpus striatum1.54e-154
striatum1.54e-154
ventral part of telencephalon1.54e-154
future corpus striatum1.54e-154
neural nucleus4.22e-149
nucleus of brain4.22e-149
anatomical conduit1.86e-12240
caudate-putamen4.78e-123
dorsal striatum4.78e-123
frontal cortex1.49e-113
anatomical cluster1.95e-09373
multi-tissue structure4.08e-09342
caudate nucleus1.43e-082
future caudate nucleus1.43e-082
organ part1.61e-08218
epithelium1.66e-08306
middle temporal gyrus2.05e-082
cell layer2.46e-08309
middle frontal gyrus2.82e-082
Ammon's horn4.31e-082
lobe parts of cerebral cortex4.31e-082
hippocampal formation4.31e-082
limbic lobe4.31e-082
amygdala4.46e-082
globus pallidus1.02e-072
pallidum1.02e-072
meninx1.53e-072
membrane organ1.53e-072
meningeal cluster1.53e-072


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)
MA0003.10.213534
MA0004.10.502801
MA0006.11.62096
MA0007.10.483857
MA0009.10.973289
MA0014.10.367415
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
MA0048.10.766755
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.0407081
MA0056.10
MA0057.11.22064
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.17.33233
MA0069.10.958358
MA0070.13.58082
MA0071.10.567661
MA0072.10.942461
MA0073.182.2519
MA0074.11.46532
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.917255
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.340955
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.13.88344
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
MA0144.12.82265
MA0145.10.0807715
MA0146.10.828373
MA0147.10.281049
MA0148.10.528066
MA0149.15.89542
MA0062.20.193221
MA0035.20.564239
MA0039.23.59026
MA0138.20.704862
MA0002.20.213296
MA0137.21.70023
MA0104.20.223944
MA0047.20.636643
MA0112.20.262665
MA0065.20.591589
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.12.27082
MA0155.10.250175
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.14.30675
MA0163.15.04376
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.226.7981
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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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