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Coexpression cluster:C927: Difference between revisions

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|full_id=C927_Lens_gall_Ciliary_mesodermal_Fibroblast_Meningeal_cholangiocellular
|full_id=C927_Lens_gall_Ciliary_mesodermal_Fibroblast_Meningeal_cholangiocellular
|id=C927
|id=C927
|ontology_enrichment_celltype=CL:0000359!7.43e-09!32;CL:0000055!7.63e-09!180;CL:0000192!2.08e-07!42;CL:0000514!2.08e-07!42;CL:0000183!3.12e-07!59
|ontology_enrichment_celltype=CL:0000055!6.66e-07!106
|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:0000477!9.39e-22!373;UBERON:0000481!3.26e-18!342;UBERON:0000119!4.08e-18!309;UBERON:0010314!7.90e-18!132;UBERON:0000483!7.13e-17!306;UBERON:0004111!9.10e-17!240;UBERON:0000025!6.37e-15!192;UBERON:0003075!2.93e-14!82;UBERON:0007284!2.93e-14!82;UBERON:0001017!6.88e-14!81;UBERON:0000955!2.02e-13!68;UBERON:0006238!2.02e-13!68;UBERON:0001016!7.70e-13!89;UBERON:0002346!1.19e-12!86;UBERON:0010371!4.99e-12!104;UBERON:0004121!6.39e-12!171;UBERON:0000924!6.39e-12!171;UBERON:0006601!6.39e-12!171;UBERON:0001049!2.21e-11!56;UBERON:0005068!2.21e-11!56;UBERON:0006241!2.21e-11!56;UBERON:0007135!2.21e-11!56;UBERON:0003056!3.66e-10!61;UBERON:0000073!4.69e-10!53;UBERON:0002616!4.69e-10!53;UBERON:0011216!6.59e-10!223;UBERON:0003528!7.12e-09!34;UBERON:0002020!7.12e-09!34;UBERON:0006876!1.00e-08!11;UBERON:0001893!1.36e-08!34;UBERON:0002791!3.34e-08!32;UBERON:0001869!4.79e-08!32;UBERON:0002780!5.19e-08!41;UBERON:0001890!5.19e-08!41;UBERON:0003080!5.19e-08!41;UBERON:0006240!5.19e-08!41;UBERON:0002050!1.21e-07!564;UBERON:0000467!2.13e-07!624;UBERON:0000922!2.20e-07!592;UBERON:0002049!2.51e-07!78;UBERON:0007798!2.51e-07!78;UBERON:0000480!2.77e-07!625;UBERON:0000468!2.93e-07!656;UBERON:0000923!4.49e-07!560;UBERON:0010316!4.49e-07!560;UBERON:0005291!4.49e-07!560;UBERON:0006598!4.49e-07!560;UBERON:0010317!4.49e-07!560;UBERON:0002532!4.49e-07!560;UBERON:0000956!6.37e-07!25;UBERON:0000203!6.37e-07!25;UBERON:0005423!8.52e-07!581
|tf_chipseq_enrich=CTBP2#1488;3:20.905666779776:0.000316544236772394:0.00324240521226678!CTCF#10664;8:4.76467233162225:1.10088565904027e-05:0.000284874621765378!E2F1#1869;8:4.3621237465594:2.18983367577486e-05:0.000481178285849465!E2F6#1876;7:3.90223223576463:0.000306742359949273:0.00316309886756933!POLR2A#5430;8:1.90884726805162:0.011661228959883:0.0425864428051338!SMARCB1#6598;8:16.2246362499177:6.9314124393577e-10:6.59899529402077e-08!ZNF263#10127;8:7.30830367734282:3.84008362723504e-07:1.87496257103693e-05
|tf_chipseq_enrich=CTBP2#1488;3:20.905666779776:0.000316544236772394:0.00324240521226678!CTCF#10664;8:4.76467233162225:1.10088565904027e-05:0.000284874621765378!E2F1#1869;8:4.3621237465594:2.18983367577486e-05:0.000481178285849465!E2F6#1876;7:3.90223223576463:0.000306742359949273:0.00316309886756933!POLR2A#5430;8:1.90884726805162:0.011661228959883:0.0425864428051338!SMARCB1#6598;8:16.2246362499177:6.9314124393577e-10:6.59899529402077e-08!ZNF263#10127;8:7.30830367734282:3.84008362723504e-07:1.87496257103693e-05
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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 16:53, 19 October 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>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell6.66e-07106
Uber Anatomy
Ontology termp-valuen
anatomical cluster9.39e-22373
multi-tissue structure3.26e-18342
cell layer4.08e-18309
structure with developmental contribution from neural crest7.90e-18132
epithelium7.13e-17306
anatomical conduit9.10e-17240
tube6.37e-15192
neural plate2.93e-1482
presumptive neural plate2.93e-1482
central nervous system6.88e-1481
brain2.02e-1368
future brain2.02e-1368
nervous system7.70e-1389
neurectoderm1.19e-1286
ecto-epithelium4.99e-12104
ectoderm-derived structure6.39e-12171
ectoderm6.39e-12171
presumptive ectoderm6.39e-12171
neural tube2.21e-1156
neural rod2.21e-1156
future spinal cord2.21e-1156
neural keel2.21e-1156
pre-chordal neural plate3.66e-1061
regional part of nervous system4.69e-1053
regional part of brain4.69e-1053
organ system subdivision6.59e-10223
brain grey matter7.12e-0934
gray matter7.12e-0934
vasculature of organ1.00e-0811
telencephalon1.36e-0834
regional part of telencephalon3.34e-0832
cerebral hemisphere4.79e-0832
regional part of forebrain5.19e-0841
forebrain5.19e-0841
anterior neural tube5.19e-0841
future forebrain5.19e-0841
embryonic structure1.21e-07564
anatomical system2.13e-07624
embryo2.20e-07592
vasculature2.51e-0778
vascular system2.51e-0778
anatomical group2.77e-07625
multi-cellular organism2.93e-07656
germ layer4.49e-07560
germ layer / neural crest4.49e-07560
embryonic tissue4.49e-07560
presumptive structure4.49e-07560
germ layer / neural crest derived structure4.49e-07560
epiblast (generic)4.49e-07560
cerebral cortex6.37e-0725
pallium6.37e-0725
developing anatomical structure8.52e-07581


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.