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Coexpression cluster:C4145: Difference between revisions

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|full_id=C4145_maxillary_gastric_caudate_medulla_Neutrophils_putamen_small
|full_id=C4145_maxillary_gastric_caudate_medulla_Neutrophils_putamen_small
|id=C4145
|id=C4145
|ontology_enrichment_celltype=CL:0002087!1.13e-16!119;CL:0000738!2.57e-16!140;CL:0002031!3.39e-13!124;CL:0002057!1.30e-09!42;CL:0000791!2.37e-09!18;CL:0000789!2.37e-09!18;CL:0002420!2.37e-09!18;CL:0002419!2.37e-09!18;CL:0000790!2.37e-09!18;CL:0000084!2.41e-09!25;CL:0000827!2.41e-09!25;CL:0000766!2.91e-09!76;CL:0002194!4.93e-09!63;CL:0000576!4.93e-09!63;CL:0000040!4.93e-09!63;CL:0000559!4.93e-09!63;CL:0002009!1.11e-08!65;CL:0000860!1.50e-07!45;CL:0000037!1.93e-07!172;CL:0000566!1.93e-07!172;CL:0000542!2.08e-07!53;CL:0000051!2.08e-07!53;CL:0000838!2.44e-07!52;CL:0000839!4.48e-07!70;CL:0002032!5.21e-07!165;CL:0000837!5.21e-07!165
|ontology_enrichment_celltype=CL:0002087!1.10e-18!115;CL:0000738!1.59e-18!136;CL:0002031!1.00e-15!120;CL:0000791!1.17e-12!18;CL:0000789!1.17e-12!18;CL:0002420!1.17e-12!18;CL:0002419!1.17e-12!18;CL:0000790!1.17e-12!18;CL:0000084!3.12e-12!25;CL:0000827!3.12e-12!25;CL:0000766!6.19e-12!72;CL:0002032!1.75e-11!161;CL:0000837!1.75e-11!161;CL:0000037!1.78e-11!168;CL:0000566!1.78e-11!168;CL:0000988!4.14e-11!177;CL:0002194!2.22e-10!59;CL:0000576!2.22e-10!59;CL:0000040!2.22e-10!59;CL:0000559!2.22e-10!59;CL:0002009!3.93e-10!61;CL:0000473!4.26e-09!48;CL:0000234!4.26e-09!48;CL:0000839!6.12e-09!66;CL:0000625!7.48e-09!11;CL:0000860!7.59e-09!42;CL:0002057!7.59e-09!42;CL:0002242!3.11e-08!55;CL:0000557!5.03e-08!67;CL:0000542!8.24e-08!53;CL:0000051!8.24e-08!53;CL:0000838!1.04e-07!52
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.28e-40!115;UBERON:0001049!1.43e-19!57;UBERON:0005068!1.43e-19!57;UBERON:0006241!1.43e-19!57;UBERON:0007135!1.43e-19!57;UBERON:0002616!1.24e-17!59;UBERON:0001017!2.70e-17!82;UBERON:0000955!3.07e-17!69;UBERON:0006238!3.07e-17!69;UBERON:0003080!7.01e-17!42;UBERON:0002780!7.78e-17!41;UBERON:0001890!7.78e-17!41;UBERON:0006240!7.78e-17!41;UBERON:0005743!2.42e-16!86;UBERON:0001893!7.12e-15!34;UBERON:0002020!9.75e-15!34;UBERON:0003528!9.75e-15!34;UBERON:0002791!2.37e-14!33;UBERON:0001869!2.41e-14!32;UBERON:0000073!3.77e-14!94;UBERON:0001016!3.77e-14!94;UBERON:0002619!3.48e-12!22;UBERON:0003075!1.52e-11!86;UBERON:0007284!1.52e-11!86;UBERON:0001950!3.52e-11!20;UBERON:0000956!2.14e-10!25;UBERON:0000203!2.14e-10!25;UBERON:0002346!5.69e-10!90;UBERON:0000153!1.03e-09!129;UBERON:0007811!1.03e-09!129;UBERON:0003056!1.88e-09!61;UBERON:0002390!4.08e-09!102;UBERON:0003061!4.08e-09!102;UBERON:0000033!1.04e-08!123;UBERON:0002193!1.14e-07!112;UBERON:0000178!1.88e-07!15;UBERON:0000179!1.88e-07!15;UBERON:0000463!1.88e-07!15
|ontology_enrichment_uberon=UBERON:0007023!1.05e-34!114;UBERON:0001049!6.03e-16!56;UBERON:0005068!6.03e-16!56;UBERON:0006241!6.03e-16!56;UBERON:0007135!6.03e-16!56;UBERON:0000073!9.51e-15!53;UBERON:0002616!9.51e-15!53;UBERON:0002780!1.74e-14!41;UBERON:0001890!1.74e-14!41;UBERON:0003080!1.74e-14!41;UBERON:0006240!1.74e-14!41;UBERON:0001893!7.34e-13!34;UBERON:0003528!1.02e-12!34;UBERON:0002020!1.02e-12!34;UBERON:0001869!2.16e-12!32;UBERON:0000955!3.01e-12!68;UBERON:0006238!3.01e-12!68;UBERON:0001017!4.33e-12!81;UBERON:0002791!5.85e-12!32;UBERON:0002390!1.16e-11!98;UBERON:0003061!1.16e-11!98;UBERON:0001016!9.02e-11!89;UBERON:0001950!1.48e-10!20;UBERON:0002619!2.44e-10!22;UBERON:0002193!8.95e-10!108;UBERON:0003075!3.41e-09!82;UBERON:0007284!3.41e-09!82;UBERON:0000178!1.86e-08!15;UBERON:0000179!1.86e-08!15;UBERON:0000463!1.86e-08!15;UBERON:0000956!3.03e-08!25;UBERON:0000203!3.03e-08!25;UBERON:0002346!4.72e-08!86;UBERON:0003056!1.35e-07!61;UBERON:0002420!6.81e-07!9;UBERON:0007245!6.81e-07!9;UBERON:0010009!6.81e-07!9;UBERON:0010011!6.81e-07!9;UBERON:0000454!6.81e-07!9
|tf_chipseq_enrich=SP2#6668;2:17.4356869958964:0.00427356848176974:0.0203217783848996!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0390232580272918
|tf_chipseq_enrich=SP2#6668;2:17.4356869958964:0.00427356848176974:0.0203217783848996!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0390232580272918
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17,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,8.47333e-05,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.0306206,0.000381649,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.0122266,0.288159,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,4.63445e-08,0.00739585,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.000797393,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.0597157,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.247324,0.178389,0.218229,0.0290303,0.0972686,0.00318326,0.0360851,0.0998546,0.131093,0.0434602,0.133616,0.418146,0.36927,0.449036,0.407369,0.231447,0.544776,0.43956,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.406019,0.381071,0.580441,0.276075,0.11074,0.366326,0.390366,0.48809,0.50058,0.443185,0.522904,2.0991e-06,0.0184337,0.227104,0.166658,0.250246,0.38649,0.284625,0.000799065,0.55194,0.375373,0.28907,0.164197,0.462688,0.0461094,0.21103,0.478174,0.00846715,0.468444,0.258219,0.446557,0.243383,0.00448654,0.390974,0.149257,0.029557,0.161598,0.0527155,0.644754,0.496032,0.00613559,0.37357,0.00106614,0.477353,6.7495e-07,0.0508568,0.00415823,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.0513026,0.314429,0.181415,0.282286,0.0192486,0.24884,0.408413,0.516511,0.322213,0.0931134,0.33942,0.61031,0.387276,0.522605,1.15611e-06,0.0433137,0.222037,0.416621,0.416292,0.128937,0.0457685,0.0019893,0.0225745,0.452428,0.138871,0.027191,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.523625,0.408861,0.365487,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.637444,0.0524515,0.0317395,0.371414,0.30666,0.303709,0.495883,0.386538,0.508064,0.250964,0.383276,0.125961,0.156714,0.220231,0.509064,0.196976,0.191517,0.463751,0.601877,0.307334,0.459728,0.283463,0.563586,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.138622,0.359231,0.339729,0.197805,0.608187,0.387069,0.332774,0.0406989,0.299887,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.0171537,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.0132793,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.0541163,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.00717361,0.261724,0.0240944,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.0352561,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.0342254,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.0164735,0.157274,0.215705,0.252796,0.205954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}}
}}

Revision as of 15:43, 19 October 2012


Full id: C4145_maxillary_gastric_caudate_medulla_Neutrophils_putamen_small



Phase1 CAGE Peaks

Hg19::chr2:175351732..175351743,-p2@GPR155
Hg19::chr2:175351744..175351828,-p1@GPR155
Hg19::chr9:12159267..12159271,+p@chr9:12159267..12159271
+


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
nongranular leukocyte1.10e-18115
leukocyte1.59e-18136
hematopoietic lineage restricted progenitor cell1.00e-15120
mature alpha-beta T cell1.17e-1218
alpha-beta T cell1.17e-1218
immature T cell1.17e-1218
mature T cell1.17e-1218
immature alpha-beta T cell1.17e-1218
T cell3.12e-1225
pro-T cell3.12e-1225
myeloid leukocyte6.19e-1272
hematopoietic oligopotent progenitor cell1.75e-11161
hematopoietic multipotent progenitor cell1.75e-11161
hematopoietic stem cell1.78e-11168
angioblastic mesenchymal cell1.78e-11168
hematopoietic cell4.14e-11177
monopoietic cell2.22e-1059
monocyte2.22e-1059
monoblast2.22e-1059
promonocyte2.22e-1059
macrophage dendritic cell progenitor3.93e-1061
defensive cell4.26e-0948
phagocyte4.26e-0948
myeloid lineage restricted progenitor cell6.12e-0966
CD8-positive, alpha-beta T cell7.48e-0911
classical monocyte7.59e-0942
CD14-positive, CD16-negative classical monocyte7.59e-0942
nucleate cell3.11e-0855
granulocyte monocyte progenitor cell5.03e-0867
lymphocyte8.24e-0853
common lymphoid progenitor8.24e-0853
lymphoid lineage restricted progenitor cell1.04e-0752
Uber Anatomy
Ontology termp-valuen
adult organism1.05e-34114
neural tube6.03e-1656
neural rod6.03e-1656
future spinal cord6.03e-1656
neural keel6.03e-1656
regional part of nervous system9.51e-1553
regional part of brain9.51e-1553
regional part of forebrain1.74e-1441
forebrain1.74e-1441
anterior neural tube1.74e-1441
future forebrain1.74e-1441
telencephalon7.34e-1334
brain grey matter1.02e-1234
gray matter1.02e-1234
cerebral hemisphere2.16e-1232
brain3.01e-1268
future brain3.01e-1268
central nervous system4.33e-1281
regional part of telencephalon5.85e-1232
hematopoietic system1.16e-1198
blood island1.16e-1198
nervous system9.02e-1189
neocortex1.48e-1020
regional part of cerebral cortex2.44e-1022
hemolymphoid system8.95e-10108
neural plate3.41e-0982
presumptive neural plate3.41e-0982
blood1.86e-0815
haemolymphatic fluid1.86e-0815
organism substance1.86e-0815
cerebral cortex3.03e-0825
pallium3.03e-0825
neurectoderm4.72e-0886
pre-chordal neural plate1.35e-0761
basal ganglion6.81e-079
nuclear complex of neuraxis6.81e-079
aggregate regional part of brain6.81e-079
collection of basal ganglia6.81e-079
cerebral subcortex6.81e-079


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
SP2#6668217.43568699589640.004273568481769740.0203217783848996
TFAP2A#7020211.01242291536330.01054990655215560.0390232580272918



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.