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Coexpression cluster:C927: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000481!3.03e-30!347;UBERON:0000477!3.77e-29!286;UBERON:0000119!7.08e-28!312;UBERON:0000475!1.69e-27!365;UBERON:0000483!1.93e-26!309;UBERON:0004111!1.61e-25!241;UBERON:0000033!2.26e-24!123;UBERON:0004121!6.77e-23!169;UBERON:0000153!2.29e-22!129;UBERON:0007811!2.29e-22!129;UBERON:0000924!3.24e-22!173;UBERON:0006601!3.24e-22!173;UBERON:0000025!5.99e-21!194;UBERON:0005743!1.26e-20!86;UBERON:0000468!4.65e-20!659;UBERON:0003075!6.92e-20!86;UBERON:0007284!6.92e-20!86;UBERON:0001017!1.16e-19!82;UBERON:0000073!2.32e-19!94;UBERON:0001016!2.32e-19!94;UBERON:0002346!8.47e-19!90;UBERON:0000955!1.34e-18!69;UBERON:0006238!1.34e-18!69;UBERON:0002616!2.58e-17!59;UBERON:0002050!3.97e-17!605;UBERON:0005423!3.97e-17!605;UBERON:0000467!4.11e-17!625;UBERON:0000922!4.25e-17!612;UBERON:0000480!6.39e-17!626;UBERON:0000923!9.44e-17!604;UBERON:0005291!9.44e-17!604;UBERON:0006598!9.44e-17!604;UBERON:0002532!9.44e-17!604;UBERON:0001049!7.37e-16!57;UBERON:0005068!7.37e-16!57;UBERON:0006241!7.37e-16!57;UBERON:0007135!7.37e-16!57;UBERON:0003056!2.43e-14!61;UBERON:0000064!2.18e-12!219;UBERON:0002780!1.95e-11!41;UBERON:0001890!1.95e-11!41;UBERON:0006240!1.95e-11!41;UBERON:0002020!2.14e-11!34;UBERON:0003528!2.14e-11!34;UBERON:0003080!2.81e-11!42;UBERON:0001893!3.19e-11!34;UBERON:0000062!3.41e-11!511;UBERON:0002791!5.00e-11!33;UBERON:0001869!7.89e-11!32;UBERON:0005256!8.91e-10!143;UBERON:0007023!1.34e-09!115;UBERON:0003104!3.53e-09!238;UBERON:0009142!3.53e-09!238;UBERON:0000956!3.72e-09!25;UBERON:0000203!3.72e-09!25;UBERON:0002049!4.57e-09!79;UBERON:0007798!4.57e-09!79;UBERON:0002100!6.95e-09!216;UBERON:0003914!2.44e-08!118;UBERON:0002619!9.59e-08!22;UBERON:0001048!2.88e-07!168;UBERON:0000914!3.34e-07!83;UBERON:0002329!3.34e-07!83;UBERON:0003077!3.34e-07!83;UBERON:0003059!3.34e-07!83;UBERON:0007282!3.34e-07!83;UBERON:0009618!3.34e-07!83;UBERON:0007285!3.34e-07!83;UBERON:0004535!3.52e-07!110;UBERON:0002200!4.15e-07!11;UBERON:0006876!4.15e-07!11;UBERON:0001134!4.67e-07!61;UBERON:0002036!4.67e-07!61;UBERON:0003082!4.67e-07!61;UBERON:0001950!4.73e-07!20;UBERON:0002385!4.83e-07!63;UBERON:0001015!4.83e-07!63;UBERON:0000383!4.83e-07!63;UBERON:0001009!6.26e-07!113
|ontology_enrichment_uberon=UBERON:0000481!3.03e-30!347;UBERON:0000477!3.77e-29!286;UBERON:0000119!7.08e-28!312;UBERON:0000475!1.69e-27!365;UBERON:0000483!1.93e-26!309;UBERON:0004111!1.61e-25!241;UBERON:0000033!2.26e-24!123;UBERON:0004121!6.77e-23!169;UBERON:0000153!2.29e-22!129;UBERON:0007811!2.29e-22!129;UBERON:0000924!3.24e-22!173;UBERON:0006601!3.24e-22!173;UBERON:0000025!5.99e-21!194;UBERON:0005743!1.26e-20!86;UBERON:0000468!4.65e-20!659;UBERON:0003075!6.92e-20!86;UBERON:0007284!6.92e-20!86;UBERON:0001017!1.16e-19!82;UBERON:0000073!2.32e-19!94;UBERON:0001016!2.32e-19!94;UBERON:0002346!8.47e-19!90;UBERON:0000955!1.34e-18!69;UBERON:0006238!1.34e-18!69;UBERON:0002616!2.58e-17!59;UBERON:0002050!3.97e-17!605;UBERON:0005423!3.97e-17!605;UBERON:0000467!4.11e-17!625;UBERON:0000922!4.25e-17!612;UBERON:0000480!6.39e-17!626;UBERON:0000923!9.44e-17!604;UBERON:0005291!9.44e-17!604;UBERON:0006598!9.44e-17!604;UBERON:0002532!9.44e-17!604;UBERON:0001049!7.37e-16!57;UBERON:0005068!7.37e-16!57;UBERON:0006241!7.37e-16!57;UBERON:0007135!7.37e-16!57;UBERON:0003056!2.43e-14!61;UBERON:0000064!2.18e-12!219;UBERON:0002780!1.95e-11!41;UBERON:0001890!1.95e-11!41;UBERON:0006240!1.95e-11!41;UBERON:0002020!2.14e-11!34;UBERON:0003528!2.14e-11!34;UBERON:0003080!2.81e-11!42;UBERON:0001893!3.19e-11!34;UBERON:0000062!3.41e-11!511;UBERON:0002791!5.00e-11!33;UBERON:0001869!7.89e-11!32;UBERON:0005256!8.91e-10!143;UBERON:0007023!1.34e-09!115;UBERON:0003104!3.53e-09!238;UBERON:0009142!3.53e-09!238;UBERON:0000956!3.72e-09!25;UBERON:0000203!3.72e-09!25;UBERON:0002049!4.57e-09!79;UBERON:0007798!4.57e-09!79;UBERON:0002100!6.95e-09!216;UBERON:0003914!2.44e-08!118;UBERON:0002619!9.59e-08!22;UBERON:0001048!2.88e-07!168;UBERON:0000914!3.34e-07!83;UBERON:0002329!3.34e-07!83;UBERON:0003077!3.34e-07!83;UBERON:0003059!3.34e-07!83;UBERON:0007282!3.34e-07!83;UBERON:0009618!3.34e-07!83;UBERON:0007285!3.34e-07!83;UBERON:0004535!3.52e-07!110;UBERON:0002200!4.15e-07!11;UBERON:0006876!4.15e-07!11;UBERON:0001134!4.67e-07!61;UBERON:0002036!4.67e-07!61;UBERON:0003082!4.67e-07!61;UBERON:0001950!4.73e-07!20;UBERON:0002385!4.83e-07!63;UBERON:0001015!4.83e-07!63;UBERON:0000383!4.83e-07!63;UBERON:0001009!6.26e-07!113
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796495,0.000451226,0.00113053,0.0431634,0.184427,0.160618,0.526429,0.22169,0.210572,0.411099,0.136624,0.155833,0.21615,0.159259,0.120131,0.100087,0.112146,0.0598938,0.428847,0.48998,0.139629,0.438323,0.750454,0.0959729,0.723796,0.000124754,0.113797,0.16848,0.0830553,0.324265,0.292348,0.29508,0.000362203,0.0833765,4.16638e-05,0.374024,0.112075,0.24008,0.156166,0.372926,0.584327,0.520077,0.132661,0.343965,0.0660153,0.049147,0.637515,0.211428,0.00276556,0.226072,0.123633,0.705997,0.380873,0.367185,0.000264112,0.365324,0.24384,0.00567028,0.6377,0.135303,0.25849,0.00959794,0.348029,0.214787,0.293114,0.338231,0.344789,0.272288,0.265858,0.147592,0.269541,0.142724,0.174255,0.209861,0.255464,0.372942,0.098628,0.206442,0.00326837,0.573908,0.218529,0.520448,0.273268,0.316704,0.473416,0.444521,0.00318686,0.16296,0.136086,0.190539,0.17172,0.439136,0.657877,0.0212774,0.00764028,0.643771,0.102996,0.331469,0.438676,0.306409,0.210704,0.500293,0.169271,0.29093,0.188743,0.292051,0.141017,0.260867,0.498927,0.210037,0.130804,0.295543,0.196359,0.536623,0.393364,0.108866,0.0688879,0.129025,0.15318,0.305064,0.253746,0.0200509,0.282957,0.528444,0.161886,0.551069,0.211069,0.00388289,0.391002,6.04685e-05,9.30944e-08,0.000344451,0.000236872,0.434353,0.355652,0.38933,0.176485,0.471182,0.084953,0.0628349,0.398405,0.200538,0.251141,0.170045,0.373446,0.38724,0.264621,0.396714,0.428823,0.0278729,4.4996e-07,0.540158,0.216165,0.020203,0.0563219,0.231141,0.701186,0.302478,0.301311,0.461915,0.438026,0.258402,0.00257295,0.576519,0.365126,0.270455,0.590817,0.279874,0.302298,0.0747253,0.423883,0.248067,0.740637,0.421922,0.4659,0.224837,0.0244708,0.399346,0.0273385,0.171188,0.167013,0.573593,0.118445,0.522209,0.545373,1.31501e-08,0.0288082,0.104396,0.215102,0.343975,0.124796,0.349674,0.803011,2.50478e-07,0.832749,0.465177,0.546036,0.0333684,0.0988169,0.750025,0.811098,0.0354712,0.483154,0.780739,0.0477885,0.790435,0.762905,1.16656e-07,0.201208,0.00185731,0.000650459,0.773427,0.0534523,0.875434,0.827364,0.025879,0.43544,0.168608,0.538296,0.375429,4.16385e-07,0.0614089,0.633899,0.00152189,0.000883196,3.76805e-08,0.272901,0.416136,0.286444,0.638875,0.0464638,0.0148684,0.348068,0.849808,0.226093,0.83048,0.56686,0.00673645,0.188067,1.89595e-05,0.00090693,0.410672,3.20808e-05,0.376241,0.15307,0.000488152,0.754179,0.0079257,0.857233,0.0946356,0.234305,0.160728,0.494538,0.488946,0.49864,0.65774,0.589099,0.00167104,0.14028,0.178728,0.39901,0.0113413,0.0778222,0.261599,2.4696e-05,0.00235572,0.415361,0.5445,0.319052,0.633308,5.73152e-05,0.677777,0.451482,0.630297,0.0901178,0.0717857,0.79296,0.00712141,0.688628,0.000130096,0.0377034,0.00017772,0.431922,0.00778457,0.0113449,0.000150195,0.529155,0.00634114,0.801122,0.28648,4.76079e-08,0.925611,0.0326442,0.539178,0.361435,0.124192,0.421792,0.000610167,0.229876,0.316091,0.049597,0.438891,0.342619,0.409234,0.383889,0.793429,0.744541,0.899287,0.0640487,0.155466,0.554076,0.494664,0.616391,0.75678,0.83052,0.726725,0.61947,0.088391,0.665579,0.201227,0.751633,0.666697,0.295828,5.80293e-05,0.769132,0.166723,0.57975,0.178712,0.114699,0.162841,0.525869,0.359628,0.482171,0.471539,0.845795,0.0619291,0.667668,0.00295746,0.632112,0.239754,0.0458311,0.452271,0.616205,0.051171,0.619062,0.76693,0.857722,0.73691,0.130485,0.483774,0.00830984,0.0171325,0.123537,0.89506,0.289804,0.00115299,0.498323,0.441318,0.21597,0.621861,0.0328605,0.0977699,0.467889,0.59289,0.465133,0.200614,0.602747,0.412715,0.470602,0.413744,0.524403,0.503232,0.24661,0.259678,0.420165,0.5818,0.172866,0.0604408,8.85071e-05,0.831057,0.119668,0.13711,0.527097,0.00752218,0.132473,0.00104196,0.521806,0.00062232,0.462243,0.326222,0.486977,0.0946253,0.254626,0.327893,0.448409,0.0012078,0.624757,0.235347,0.00913764,0.503902,0.0112809,0.529704,0.188703,0.504091,0.605432,0.302353,0.37651,0.54245,0.00217058,0.0445938,0.425621,0.111096,0.18548,0.148563,0.130525,0.608967,0.49107,0.141608,0.396522,0.318983,0.267772,0.291371,0.0150229,0.51798,0.40407,0.52603,0.478764,0.328268,0.594172,0.100432,0.022876,0.40705,0.590314,0.387463,0.000970161,0.00776029,0.457295,0.126843,0.201671,0.226502,0.00246173,0.00530146,0.51408,0.00569438,0.368078,0.474502,0.212719,0.00058075,0.177976,0.571519,0.434445,0.488829,0.363467,0.482434,0.561852,0.399782,0.343945,0.0130201,0.0413289,0.111066,0.44213,0.263525,0.148007,0.672069,0.628217,0.522084,0.226979,0.491955,0.287253,0.152349,0.0123189,0.38832,0.0252807,0.117262,0.152699,0.685459,0.597602,0.50945,0.46408,0.190581,0.132054,0.22458,0.266409,0.180355,0.322962,0.179632,0.282128,0.186072,0.211757,0.338622,0.0478864,0.126579,0.187708,0.245457,0.106235,0.352719,0.496388,0.650742,0.0198285,5.73753e-05,0.367773,0.599943,0.588096,0.488202,0.538989,0.0922562,0.584019,0.021833,0.0190347,0.0145351,0.345488,0.408688,0.499886,0.00485603,0.00388471,0.554869,0.692656,0.308763,0.521884,0.532407,0.307503,0.478305,0.470512,0.629431,0.631734,0.578048,0.41706,0.533176,0.00342706,0.0329767,0.179608,0.502814,0.00367886,0.236266,0.6812,0.431685,0.404852,0.613018,0.198522,0.0707484,0.273479,0.530083,0.0212343,0.401506,0.517565,0.0586842,0.152975,0.739615
}}
}}

Revision as of 14:07, 5 September 2012


Full id: C927_Lens_gall_Ciliary_mesodermal_Fibroblast_Meningeal_cholangiocellular



Phase1 CAGE Peaks

Hg19::chr1:12416343..12416350,+p@chr1:12416343..12416350
+
Hg19::chr1:218519119..218519130,+p16@TGFB2
Hg19::chr1:218519150..218519159,+p20@TGFB2
Hg19::chr1:218519166..218519227,+p4@TGFB2
Hg19::chr1:218519393..218519489,+p2@TGFB2
Hg19::chr1:218519541..218519558,+p14@TGFB2
Hg19::chr1:218519582..218519594,+p8@TGFB2
Hg19::chr1:218519607..218519630,+p5@TGFB2
Hg19::chr1:218519642..218519668,+p3@TGFB2


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
multi-tissue structure3.03e-30347
anatomical cluster3.77e-29286
cell layer7.08e-28312
organism subdivision1.69e-27365
epithelium1.93e-26309
anatomical conduit1.61e-25241
head2.26e-24123
ectoderm-derived structure6.77e-23169
anterior region of body2.29e-22129
craniocervical region2.29e-22129
ectoderm3.24e-22173
presumptive ectoderm3.24e-22173
tube5.99e-21194
multi-cellular organism4.65e-20659
neural plate6.92e-2086
presumptive neural plate6.92e-2086
central nervous system1.16e-1982
regional part of nervous system2.32e-1994
nervous system2.32e-1994
neurectoderm8.47e-1990
brain1.34e-1869
future brain1.34e-1869
regional part of brain2.58e-1759
embryonic structure3.97e-17605
developing anatomical structure3.97e-17605
anatomical system4.11e-17625
embryo4.25e-17612
anatomical group6.39e-17626
germ layer9.44e-17604
embryonic tissue9.44e-17604
presumptive structure9.44e-17604
epiblast (generic)9.44e-17604
neural tube7.37e-1657
neural rod7.37e-1657
future spinal cord7.37e-1657
neural keel7.37e-1657
pre-chordal neural plate2.43e-1461
organ part2.18e-12219
regional part of forebrain1.95e-1141
forebrain1.95e-1141
future forebrain1.95e-1141
gray matter2.14e-1134
brain grey matter2.14e-1134
anterior neural tube2.81e-1142
telencephalon3.19e-1134
organ3.41e-11511
regional part of telencephalon5.00e-1133
cerebral hemisphere7.89e-1132
trunk mesenchyme8.91e-10143
adult organism1.34e-09115
mesenchyme3.53e-09238
entire embryonic mesenchyme3.53e-09238
cerebral cortex3.72e-0925
pallium3.72e-0925
vasculature4.57e-0979
vascular system4.57e-0979
trunk6.95e-09216
epithelial tube2.44e-08118
regional part of cerebral cortex9.59e-0822
primordium2.88e-07168
somite3.34e-0783
paraxial mesoderm3.34e-0783
presomitic mesoderm3.34e-0783
presumptive segmental plate3.34e-0783
trunk paraxial mesoderm3.34e-0783
presumptive paraxial mesoderm3.34e-0783
cardiovascular system3.52e-07110
vasculature of head4.15e-0711
vasculature of organ4.15e-0711
skeletal muscle tissue4.67e-0761
striated muscle tissue4.67e-0761
myotome4.67e-0761
neocortex4.73e-0720
muscle tissue4.83e-0763
musculature4.83e-0763
musculature of body4.83e-0763
circulatory system6.26e-07113


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)

{{{tfbs_overrepresentation_jaspar}}}



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
CTBP2#1488320.9056667797760.0003165442367723940.00324240521226678
CTCF#1066484.764672331622251.10088565904027e-050.000284874621765378
E2F1#186984.36212374655942.18983367577486e-050.000481178285849465
E2F6#187673.902232235764630.0003067423599492730.00316309886756933
POLR2A#543081.908847268051620.0116612289598830.0425864428051338
SMARCB1#6598816.22463624991776.9314124393577e-106.59899529402077e-08
ZNF263#1012787.308303677342823.84008362723504e-071.87496257103693e-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.