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Coexpression cluster:C3891: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!9.65e-16!56;UBERON:0005068!9.65e-16!56;UBERON:0006241!9.65e-16!56;UBERON:0007135!9.65e-16!56;UBERON:0000073!4.51e-14!53;UBERON:0002616!4.51e-14!53;UBERON:0000468!5.24e-14!656;UBERON:0000467!3.03e-13!624;UBERON:0000480!3.19e-13!625;UBERON:0001017!1.36e-12!81;UBERON:0002780!6.19e-12!41;UBERON:0001890!6.19e-12!41;UBERON:0003080!6.19e-12!41;UBERON:0006240!6.19e-12!41;UBERON:0003528!8.35e-12!34;UBERON:0002020!8.35e-12!34;UBERON:0002050!1.61e-11!564;UBERON:0000923!1.65e-11!560;UBERON:0010316!1.65e-11!560;UBERON:0005291!1.65e-11!560;UBERON:0006598!1.65e-11!560;UBERON:0010317!1.65e-11!560;UBERON:0002532!1.65e-11!560;UBERON:0003075!2.20e-11!82;UBERON:0007284!2.20e-11!82;UBERON:0001893!2.30e-11!34;UBERON:0002791!5.26e-11!32;UBERON:0010314!5.54e-11!132;UBERON:0001869!1.40e-10!32;UBERON:0001016!1.99e-10!89;UBERON:0005423!2.27e-10!581;UBERON:0002346!2.35e-10!86;UBERON:0000955!2.46e-10!68;UBERON:0006238!2.46e-10!68;UBERON:0000922!4.89e-10!592;UBERON:0010371!5.31e-10!104;UBERON:0000062!1.14e-08!503;UBERON:0000926!1.22e-08!315;UBERON:0004120!1.22e-08!315;UBERON:0006603!1.22e-08!315;UBERON:0004111!2.00e-08!240;UBERON:0000025!2.47e-08!192;UBERON:0000956!3.53e-08!25;UBERON:0000203!3.53e-08!25;UBERON:0003056!3.61e-08!61;UBERON:0004121!7.74e-08!171;UBERON:0000924!7.74e-08!171;UBERON:0006601!7.74e-08!171;UBERON:0002619!3.11e-07!22;UBERON:0007023!3.33e-07!114
|ontology_enrichment_uberon=UBERON:0001049!9.65e-16!56;UBERON:0005068!9.65e-16!56;UBERON:0006241!9.65e-16!56;UBERON:0007135!9.65e-16!56;UBERON:0000073!4.51e-14!53;UBERON:0002616!4.51e-14!53;UBERON:0000468!5.24e-14!656;UBERON:0000467!3.03e-13!624;UBERON:0000480!3.19e-13!625;UBERON:0001017!1.36e-12!81;UBERON:0002780!6.19e-12!41;UBERON:0001890!6.19e-12!41;UBERON:0003080!6.19e-12!41;UBERON:0006240!6.19e-12!41;UBERON:0003528!8.35e-12!34;UBERON:0002020!8.35e-12!34;UBERON:0002050!1.61e-11!564;UBERON:0000923!1.65e-11!560;UBERON:0010316!1.65e-11!560;UBERON:0005291!1.65e-11!560;UBERON:0006598!1.65e-11!560;UBERON:0010317!1.65e-11!560;UBERON:0002532!1.65e-11!560;UBERON:0003075!2.20e-11!82;UBERON:0007284!2.20e-11!82;UBERON:0001893!2.30e-11!34;UBERON:0002791!5.26e-11!32;UBERON:0010314!5.54e-11!132;UBERON:0001869!1.40e-10!32;UBERON:0001016!1.99e-10!89;UBERON:0005423!2.27e-10!581;UBERON:0002346!2.35e-10!86;UBERON:0000955!2.46e-10!68;UBERON:0006238!2.46e-10!68;UBERON:0000922!4.89e-10!592;UBERON:0010371!5.31e-10!104;UBERON:0000062!1.14e-08!503;UBERON:0000926!1.22e-08!315;UBERON:0004120!1.22e-08!315;UBERON:0006603!1.22e-08!315;UBERON:0004111!2.00e-08!240;UBERON:0000025!2.47e-08!192;UBERON:0000956!3.53e-08!25;UBERON:0000203!3.53e-08!25;UBERON:0003056!3.61e-08!61;UBERON:0004121!7.74e-08!171;UBERON:0000924!7.74e-08!171;UBERON:0006601!7.74e-08!171;UBERON:0002619!3.11e-07!22;UBERON:0007023!3.33e-07!114
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323,0.173708,0.141119,0.0241568,0.0300692,0.131551,0.0445237,0.052362,0.0235128,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.0241929,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.549354,0.000564671,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.0458479,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.323837,0.120459,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.0425274,0.047822,0.655293,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.0163547,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.00824114,0.175094,0.43617,0.936279,0.206454,0.218192,0.108277,0.0673484,0.00613985,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.0277579,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.00259914,0.0759837,0.0457643,0.152372,0.0203723,0.218271,0.101607,0.327067,0.000990951,0.000904138,0.151597,0.0626744,0.00136247,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.000479913,0.228144,0.251466,0.288096,0.00738316,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.000223227,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.220462,0.166967,0.0190329,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.0743925,0.0360851,0.412187,0.131093,0.0434602,0.00935312,0.103051,0.0785808,0.449036,0.00206189,0.0291288,0.00131394,0.00296095,0.37006,0.10748,0.120472,0.197484,0.0919774,0.0750251,0.406019,0.381071,0.580441,0.00417723,0.432035,0.0100497,0.0886602,0.48809,0.153829,0.443185,0.00100396,0.616975,0.60734,0.227104,0.518585,0.00310917,0.0135352,0.284625,0.504757,0.00143312,0.0108655,0.28907,0.164197,0.128922,0.287881,0.574635,0.478174,0.336276,0.00403041,0.258219,3.5958e-05,0.243383,0.0659137,0.390974,0.0115792,0.000194132,0.161598,0.0527155,0.0868402,0.496032,0.476802,0.0805771,0.200632,0.477353,0.78384,0.0132585,0.185744,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.0720718,0.0142192,0.230581,0.120226,0.0448825,0.20075,0.0556238,0.181415,0.0442318,0.194707,0.0727621,0.000215097,0.165147,0.322213,0.00480191,0.000885969,0.61031,0.00162648,0.00100024,0.802166,0.180745,0.222037,0.416621,0.416292,0.462712,0.0115406,0.579431,0.204817,0.452428,0.138871,0.308032,0.000885521,0.19783,0.0833851,0.00691922,0.0289164,0.175199,0.332919,0.00137548,0.0393909,0.0980968,0.0768488,0.534741,0.0889149,0.363192,0.0303438,0.203486,0.273398,0.375787,0.0223007,0.0704514,0.0419637,0.637444,0.00618487,0.0317395,0.0795725,0.30666,0.00604105,0.0323359,0.386538,0.159081,0.250964,0.383276,0.00360665,0.504711,0.0262575,0.00608438,0.196976,0.191517,0.129584,0.0663581,0.307334,0.459728,0.283463,0.201728,0.135386,0.399569,0.273281,0.368095,0.0418805,0.384593,0.000564944,0.00114842,0.339729,0.197805,0.0153645,0.0136044,0.332774,0.52832,0.0502872,8.64162e-05,0.205413,0.17639,0.0779009,0.0424553,0.205298,0.0337138,0.18966,0.00358475,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.0269454,0.341681,0.310674,0.21801,0.0211771,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.0233967,0.0335483,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.0126763,0.120196,0.0986735,0.000231458,0.0595618,0.0251995,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,1.14841e-05,2.46912e-06,0.185335,0.0723291,0.0367308,0.261744,0.203781,0.000115216,0.207559,0.141867,0.0199603,0.249101,0.115972,0.224568,0.0331281,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.00899301,0.256963,0.0269005,0.0157468,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.00347819,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.000840685,0.0537355,0.000677683,0.0377035,0.211332,0.0012829,0.233626,0.189559,0.0812887,0.0981146,0.00210274,0.0077532,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.00618871,0.04411,0.066952,0.00414049,0.0367455,0.13497,0.00168003,0.295769,0.286691,0.0687209,0.141729,1.71764e-05,0.00345643,0.00157056,0.227491,0.29837,0.253509,0.177664,0.00039571,0.264413,0.131761,0.160658,0.206239,0.021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|tfbs_overrepresentation_for_novel_motifs=0.699513,1.40091,0.690871,0.855819,1.54806,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,1.14835,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.843849,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,1.54087,0.461452,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,1.25415,0.333216,1.45054,0.430728,1.06461,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,1.24629,1.39759,0.169933,1.48681,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,2.14531,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,1.76124,0.710709,1.56892,1.35169,1.19946,2.85375,1.11698,0.960047,0.524529,0.936473,0.0768232
}}
}}

Revision as of 16:25, 26 November 2012


Full id: C3891_occipital_Osteoblast_Preadipocyte_spinal_leiomyoma_duodenum_Monocytederived



Phase1 CAGE Peaks

Hg19::chr1:160182958..160182971,+p@chr1:160182958..160182971
+
Hg19::chr1:160182997..160183029,+p@chr1:160182997..160183029
+
Hg19::chr1:160183342..160183398,+p6@PEA15


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
defensive cell3.27e-0748
phagocyte3.27e-0748
classical monocyte6.81e-0742
CD14-positive, CD16-negative classical monocyte6.81e-0742
Uber Anatomy
Ontology termp-valuen
neural tube9.65e-1656
neural rod9.65e-1656
future spinal cord9.65e-1656
neural keel9.65e-1656
regional part of nervous system4.51e-1453
regional part of brain4.51e-1453
multi-cellular organism5.24e-14656
anatomical system3.03e-13624
anatomical group3.19e-13625
central nervous system1.36e-1281
regional part of forebrain6.19e-1241
forebrain6.19e-1241
anterior neural tube6.19e-1241
future forebrain6.19e-1241
brain grey matter8.35e-1234
gray matter8.35e-1234
embryonic structure1.61e-11564
germ layer1.65e-11560
germ layer / neural crest1.65e-11560
embryonic tissue1.65e-11560
presumptive structure1.65e-11560
germ layer / neural crest derived structure1.65e-11560
epiblast (generic)1.65e-11560
neural plate2.20e-1182
presumptive neural plate2.20e-1182
telencephalon2.30e-1134
regional part of telencephalon5.26e-1132
structure with developmental contribution from neural crest5.54e-11132
cerebral hemisphere1.40e-1032
nervous system1.99e-1089
developing anatomical structure2.27e-10581
neurectoderm2.35e-1086
brain2.46e-1068
future brain2.46e-1068
embryo4.89e-10592
ecto-epithelium5.31e-10104
organ1.14e-08503
mesoderm1.22e-08315
mesoderm-derived structure1.22e-08315
presumptive mesoderm1.22e-08315
anatomical conduit2.00e-08240
tube2.47e-08192
cerebral cortex3.53e-0825
pallium3.53e-0825
pre-chordal neural plate3.61e-0861
ectoderm-derived structure7.74e-08171
ectoderm7.74e-08171
presumptive ectoderm7.74e-08171
regional part of cerebral cortex3.11e-0722
adult organism3.33e-07114


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

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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