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Coexpression cluster:C623: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0035300!inositol trisphosphate 5/6-kinase activity!0.0113730683144134!3705$GO:0043647!inositol phosphate metabolic process!0.0113730683144134!3705$GO:0051765!inositol tetrakisphosphate kinase activity!0.0113730683144134!3705$GO:0032957!inositol trisphosphate metabolic process!0.0113730683144134!3705$GO:0047325!inositol tetrakisphosphate 1-kinase activity!0.0113730683144134!3705$GO:0022610!biological adhesion!0.0142547691685994!3684;50856;397$GO:0007155!cell adhesion!0.0142547691685994!3684;50856;397$GO:0001948!glycoprotein binding!0.0213169715519573!3684$GO:0048268!clathrin cage assembly!0.0227340873511213!8301$GO:0006901!vesicle coating!0.0227340873511213!8301$GO:0006900!membrane budding!0.02324871800575!8301$GO:0030276!clathrin binding!0.0260425749057417!8301$GO:0006020!inositol metabolic process!0.0266215290817958!3705$GO:0051766!inositol trisphosphate kinase activity!0.0266215290817958!3705$GO:0031410!cytoplasmic vesicle!0.0266215290817958!8301;397$GO:0031982!vesicle!0.0266215290817958!8301;397$GO:0016050!vesicle organization and biogenesis!0.0266215290817958!8301$GO:0000287!magnesium ion binding!0.0266215290817958!3705;3684$GO:0005545!phosphatidylinositol binding!0.0269705183200261!8301$GO:0005094!Rho GDP-dissociation inhibitor activity!0.0269705183200261!397$GO:0007162!negative regulation of cell adhesion!0.0351278293777307!397$GO:0005092!GDP-dissociation inhibitor activity!0.036104050016986!397$GO:0006898!receptor-mediated endocytosis!0.0487274734501486!8301$GO:0044459!plasma membrane part!0.0487274734501486!8301;3684;50856$GO:0005905!coated pit!0.0487274734501486!8301
|gostat_on_coexpression_clusters=GO:0035300!inositol trisphosphate 5/6-kinase activity!0.0113730683144134!3705$GO:0043647!inositol phosphate metabolic process!0.0113730683144134!3705$GO:0051765!inositol tetrakisphosphate kinase activity!0.0113730683144134!3705$GO:0032957!inositol trisphosphate metabolic process!0.0113730683144134!3705$GO:0047325!inositol tetrakisphosphate 1-kinase activity!0.0113730683144134!3705$GO:0022610!biological adhesion!0.0142547691685994!3684;50856;397$GO:0007155!cell adhesion!0.0142547691685994!3684;50856;397$GO:0001948!glycoprotein binding!0.0213169715519573!3684$GO:0048268!clathrin cage assembly!0.0227340873511213!8301$GO:0006901!vesicle coating!0.0227340873511213!8301$GO:0006900!membrane budding!0.02324871800575!8301$GO:0030276!clathrin binding!0.0260425749057417!8301$GO:0006020!inositol metabolic process!0.0266215290817958!3705$GO:0051766!inositol trisphosphate kinase activity!0.0266215290817958!3705$GO:0031410!cytoplasmic vesicle!0.0266215290817958!8301;397$GO:0031982!vesicle!0.0266215290817958!8301;397$GO:0016050!vesicle organization and biogenesis!0.0266215290817958!8301$GO:0000287!magnesium ion binding!0.0266215290817958!3705;3684$GO:0005545!phosphatidylinositol binding!0.0269705183200261!8301$GO:0005094!Rho GDP-dissociation inhibitor activity!0.0269705183200261!397$GO:0007162!negative regulation of cell adhesion!0.0351278293777307!397$GO:0005092!GDP-dissociation inhibitor activity!0.036104050016986!397$GO:0006898!receptor-mediated endocytosis!0.0487274734501486!8301$GO:0044459!plasma membrane part!0.0487274734501486!8301;3684;50856$GO:0005905!coated pit!0.0487274734501486!8301
|id=C623
|id=C623
|ontology_enrichment_celltype=CL:0000763!7.94e-45!112;CL:0000049!7.94e-45!112;CL:0000766!6.53e-41!76;CL:0000557!5.07e-37!71;CL:0000839!1.88e-35!70;CL:0002009!3.24e-34!65;CL:0000037!5.38e-34!172;CL:0000566!5.38e-34!172;CL:0002194!3.48e-33!63;CL:0000576!3.48e-33!63;CL:0000040!3.48e-33!63;CL:0000559!3.48e-33!63;CL:0002032!4.28e-32!165;CL:0000837!4.28e-32!165;CL:0000988!7.08e-30!182;CL:0000738!2.22e-28!140;CL:0002057!1.49e-25!42;CL:0000860!3.06e-25!45;CL:0002031!4.36e-22!124;CL:0002087!1.78e-20!119;CL:0000134!7.87e-08!358;CL:0002393!9.66e-07!9;CL:0002397!9.66e-07!9
|ontology_enrichment_celltype=CL:0000766!3.78e-66!72;CL:0002009!2.71e-62!61;CL:0002194!2.09e-60!59;CL:0000576!2.09e-60!59;CL:0000040!2.09e-60!59;CL:0000559!2.09e-60!59;CL:0000473!4.41e-57!48;CL:0000234!4.41e-57!48;CL:0000557!1.73e-56!67;CL:0000839!1.88e-53!66;CL:0000860!1.12e-49!42;CL:0002057!1.12e-49!42;CL:0000738!2.84e-42!136;CL:0000763!1.39e-41!108;CL:0000049!1.39e-41!108;CL:0002087!1.74e-34!115;CL:0002031!1.37e-31!120;CL:0000037!6.35e-31!168;CL:0000566!6.35e-31!168;CL:0000988!5.75e-28!177;CL:0002032!6.07e-28!161;CL:0000837!6.07e-28!161;CL:0000325!3.03e-24!87;CL:0002393!6.56e-12!9;CL:0002397!6.56e-12!9;CL:0000094!2.49e-11!8;CL:0000235!1.39e-08!6;CL:0000840!3.87e-08!5;CL:0001029!3.87e-08!5;CL:0000081!1.26e-07!11
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!1.15e-34!102;UBERON:0003061!1.15e-34!102;UBERON:0002193!1.43e-33!112;UBERON:0007023!1.08e-30!115;UBERON:0002371!1.49e-29!80;UBERON:0001474!1.91e-26!86;UBERON:0003081!1.14e-25!216;UBERON:0002405!1.52e-21!115;UBERON:0004765!7.85e-19!101;UBERON:0001434!7.85e-19!101;UBERON:0002204!1.36e-13!167;UBERON:0000479!3.38e-09!787;UBERON:0001049!6.13e-09!57;UBERON:0005068!6.13e-09!57;UBERON:0006241!6.13e-09!57;UBERON:0007135!6.13e-09!57;UBERON:0003080!1.20e-07!42;UBERON:0002780!1.87e-07!41;UBERON:0001890!1.87e-07!41;UBERON:0006240!1.87e-07!41;UBERON:0002616!3.10e-07!59;UBERON:0001893!7.63e-07!34;UBERON:0002020!8.81e-07!34;UBERON:0003528!8.81e-07!34
|ontology_enrichment_uberon=UBERON:0002390!2.43e-59!98;UBERON:0003061!2.43e-59!98;UBERON:0002193!1.36e-54!108;UBERON:0002371!3.25e-47!76;UBERON:0002405!2.63e-43!93;UBERON:0001474!3.53e-42!82;UBERON:0004765!1.57e-36!90;UBERON:0007023!1.82e-34!114;UBERON:0001434!4.93e-32!100;UBERON:0003081!4.74e-22!203;UBERON:0002204!4.21e-15!167;UBERON:0000178!1.13e-11!15;UBERON:0000179!1.13e-11!15;UBERON:0000463!1.13e-11!15;UBERON:0000926!3.81e-11!315;UBERON:0004120!3.81e-11!315;UBERON:0006603!3.81e-11!315;UBERON:0001049!2.22e-08!56;UBERON:0005068!2.22e-08!56;UBERON:0006241!2.22e-08!56;UBERON:0007135!2.22e-08!56;UBERON:0000479!8.71e-08!773;UBERON:0000923!1.10e-07!560;UBERON:0010316!1.10e-07!560;UBERON:0005291!1.10e-07!560;UBERON:0006598!1.10e-07!560;UBERON:0010317!1.10e-07!560;UBERON:0002532!1.10e-07!560;UBERON:0002050!2.15e-07!564;UBERON:0000073!5.45e-07!53;UBERON:0002616!5.45e-07!53;UBERON:0001893!5.98e-07!34;UBERON:0005423!7.68e-07!581
|tf_chipseq_enrich=NFE2#4778;2:11.0291800930899:0.0137623173564868:0.0484452682056733!SPI1#6688;7:4.10216175426136:0.000625554480566112:0.005149545550236
|tf_chipseq_enrich=NFE2#4778;2:11.0291800930899:0.0137623173564868:0.0484452682056733!SPI1#6688;7:4.10216175426136:0.000625554480566112:0.005149545550236
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561,0.323854,0.322854,0.307749,0.199738,0.0806561,0.231656,0.315342,0.236502,0.180519,0.151296,0.168921,0.746322,0.058209,0.0892168,0.208593,0.226526,0.0681666,0.145253,0.14313,0.111289,0.171324,0.249488,0.113702,0.456489,0.416036,0.419538,0.756891,0.126655,0.316582,0.517459,0.168817,0.34758,0.232128,0.516141,0.396218,0.00116983,0.0180015,0.140572,0.677803,0.134439,0.793723,0.308916,0.586693,0.328776,0.242733,0.0444279,0.525647,0.0355913,0.574376,0.506986,0.0711139,0.515659,0.211314,0.202394,0.372,0.00217163,0.48593,0.313489,0.102442,0.473863,0.481952,0.30234,0.0235874,0.219957,0.0867583,0.213016,0.257581,0.306778,0.368009,0.516161,0.149154,0.302107,0.446917,0.295564,0.00521245,0.681197,0.796833,0.447,0.631254,0.599302,0.506727,0.241724,0.203517,0.411776,0.254032,0.593244,0.496898,0.0475166,0.331119,0.476881,0.15556,0.465476,0.592725,0.00147275,0.0386946,0.660112,0.318751,0.414214,0.277745,0.415655,0.0239159,0.375129,0.291768,0.307018,0.19593,0.10413,0.288264,0.697766,0.54045,0.16414,0.485192,0.193367,0.0282023,0.432278,0.365739,0.58654,0.403936,0.689428,0.002816,0.712296,0.053384,0.00565634,0.180988,0.268626,0.109678,0.393482,0.011696,0.587836,0.133213,0.0428228,0.260698,0.260953,0.173572,0.233363,0.546377,0.294013,0.362292,0.251684,0.165331,0.533214,0.380058,0.186228,0.216998,0.265882,0.497808,0.000261872,0.741186,0.470466,0.446456,0.0639472,0.121731,0.428988,0.427501,0.0738067,0.000336481,0.371883,0.174031,0.151399,0.506747,0.387692,0.0526076,0.399946,0.428759,0.113799,0.00190823,0.358215,0.587702,0.0552678,0.00329935,0.327109,0.0163158,0.0464104,0.520337,0.245964,0.247428,0.734435,0.233724,0.109626,0.126246,0.229854,0.0174249,0.157609,0.238076,0.0289807,0.187268,0.487947,0.248246,0.0672787,0.526182,0.0382285,0.707263,0.0794078,0.137413,0.634728,0.0169283,0.063355,0.641807,0.682869,0.618648,0.438344,0.387698,0.576862,0.351932,0.740229,0.000167216,0.202591,0.818737,0.11003,0.293072,0.136303,0.273886,0.00952743,0.699462,0.0234746,0.0397541,0.398636,0.20715,0.0191388,0.0859677,0.162791,0.214622,0.567003,0.0740631,0.470009,0.0504875,0.0353196,0.569882,0.176256,0.751904,0.00221731,0.727883,0.000972869,0.407716,0.00476294,0.0945002,0.560684,0.000148884,0.0575446,0.39699,0.000298993,0.177253,0.00304754,0.0867628,0.00684854,0.0310932,0.257848,0.654004,0.088611,0.00492527,0.00732576,0.749305,0.00521969,0.86528,0.0786534,0.188354,0.508845,0.105858,0.376091,0.259157,0.605993,0.566109,0.0358187,0.449954,0.206507,0.897351,0.828244,0.0685992,0.0717926,0.028778,0.0389398,0.0387485,0.0572389,0.273391,0.873768,0.0143295,0.00566881,0.0821136,0.00300322,0.0828941,0.155465,0.114432,0.460016,0.042849,0.168066,0.0509523,0.115098,0.289796,0.939828,0.50228,0.0836584,0.573511,0.274797,0.0632536,0.0346605,0.0898256,0.592968,0.563195,0.00716206,0.0252487,0.232486,0.0644178,0.287978,0.00964227,0.162494,0.715288,0.654138,0.774723,0.645241,0.146323,0.328191,0.443165,0.0035894,0.818025,0.368799,0.368331,0.245179,0.0915919,0.00567446,0.0814651,0.421994,0.740375,0.392144,0.161355,0.83881,0.686786,0.644586,0.640746,0.629207,0.555901,0.263001,0.510977,0.781093,0.460581,0.0177247,0.0116617,0.907496,0.774553,0.0663809,0.777159,0.896226,0.80577,0.614452,0.306319,0.642475,0.811568,0.0819317,0.0431341,0.275837,0.810569,0.0220722,0.658026,0.595703,0.315097,0.779701,0.290833,0.147894,0.0178692,0.166003,0.622192,0.294118,0.420552,0.56305,0.0183426,0.56424,0.685278,0.296691,0.356279,0.373564,0.571642,0.742343,0.382247,0.747657,0.662256,0.14708,0.602579,0.633647,0.688046,0.329164,0.857865,0.517909,0.109352,0.276474,0.619012,0.00364702,0.278303,0.14327,0.366902,0.461022,0.0671165,0.337649,0.78232,0.0662792,0.481022,0.663924,0.734869,0.690717,0.277689,0.664123,0.0591212,0.428828,0.168016,0.703657,0.56202,0.702807,0.577896,0.167392,0.27322,0.22134,0.195528,0.428906,0.650305,0.0538856,0.186051,0.449866,0.384185,0.414781,0.249171,0.313836,0.553004,0.112251,0.637063,0.46149,0.754102,0.0958472,0.605271,0.556477,0.750457,0.533477,0.680896,0.460642,0.613545,0.61579,0.295569,0.752335,0.757358,0.287565,0.674587,0.662315,0.51031,0.632436,0.737348,0.11382,0.694833,0.147133,0.587939,0.00437738,0.504741,0.64103,0.722973,0.547991,0.480913,0.749937,0.69157,0.58586,0.0641588,0.378621,0.651396,0.251876,0.785434,0.10954,0.329999,0.283877,0.409482,0.226719,0.227361,0.534493,0.315496,0.176359,0.227215,0.0363504,0.170393,0.669752,0.621034,0.0375025,0.257188,0.326761,0.382401,0.0390425,0.454858,0.265087,0.402864,0.274042,0.309364,0.474347,0.416949,0.189841,0.276311,0.354746,0.160298,0.491672,0.655972,0.805312,0.0756202,0.140913,0.509942,0.056599,0.748352,0.647234,0.339005,0.0863771,0.744466,0.598612,0.460981,0.761425,0.482811,0.000206565,0.659682,0.64545,0.0757958,0.358601,0.840422,0.0206641,0.318447,0.693478,0.435373,0.268713,0.628086,0.786522,0.0725914,0.388065,0.568069,0.694262,0.367768,0.117266,0.697002,0.662776,0.375214,0.342479,0.530675,0.219847,0.193816,0.434383,0.291242,0.432933,0.391636,0.691105,0.0633558,0.190679,0.678211,0.394262,0.292248,0.618619
}}
}}

Revision as of 16:30, 19 October 2012


Full id: C623_Dendritic_Neutrophils_Eosinophils_Whole_Macrophage_CD14_Basophils



Phase1 CAGE Peaks

Hg19::chr11:85779986..85780014,-p3@PICALM
Hg19::chr11:85780015..85780042,-p2@PICALM
Hg19::chr12:15114191..15114233,-p5@ARHGDIB
Hg19::chr12:8276205..8276219,+p2@CLEC4A
Hg19::chr12:8276224..8276237,+p3@CLEC4A
Hg19::chr14:93581500..93581509,-p12@ITPK1
Hg19::chr16:28192360..28192372,-p3@AB384470
Hg19::chr16:31271322..31271339,+p2@ITGAM
Hg19::chr16:8738211..8738249,+p@chr16:8738211..8738249
+
Hg19::chr16:8738462..8738501,+p@chr16:8738462..8738501
+
Hg19::chr16:90023641..90023698,+p@chr16:90023641..90023698
+
Hg19::chr3:149531627..149531651,+p7@RNF13
Hg19::chr5:142193841..142193874,+p@chr5:142193841..142193874
+
Hg19::chr8:38662960..38663003,+p9@TACC1


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:0035300inositol trisphosphate 5/6-kinase activity0.0113730683144134
GO:0043647inositol phosphate metabolic process0.0113730683144134
GO:0051765inositol tetrakisphosphate kinase activity0.0113730683144134
GO:0032957inositol trisphosphate metabolic process0.0113730683144134
GO:0047325inositol tetrakisphosphate 1-kinase activity0.0113730683144134
GO:0022610biological adhesion0.0142547691685994
GO:0007155cell adhesion0.0142547691685994
GO:0001948glycoprotein binding0.0213169715519573
GO:0048268clathrin cage assembly0.0227340873511213
GO:0006901vesicle coating0.0227340873511213
GO:0006900membrane budding0.02324871800575
GO:0030276clathrin binding0.0260425749057417
GO:0006020inositol metabolic process0.0266215290817958
GO:0051766inositol trisphosphate kinase activity0.0266215290817958
GO:0031410cytoplasmic vesicle0.0266215290817958
GO:0031982vesicle0.0266215290817958
GO:0016050vesicle organization and biogenesis0.0266215290817958
GO:0000287magnesium ion binding0.0266215290817958
GO:0005545phosphatidylinositol binding0.0269705183200261
GO:0005094Rho GDP-dissociation inhibitor activity0.0269705183200261
GO:0007162negative regulation of cell adhesion0.0351278293777307
GO:0005092GDP-dissociation inhibitor activity0.036104050016986
GO:0006898receptor-mediated endocytosis0.0487274734501486
GO:0044459plasma membrane part0.0487274734501486
GO:0005905coated pit0.0487274734501486



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
myeloid leukocyte3.78e-6672
macrophage dendritic cell progenitor2.71e-6261
monopoietic cell2.09e-6059
monocyte2.09e-6059
monoblast2.09e-6059
promonocyte2.09e-6059
defensive cell4.41e-5748
phagocyte4.41e-5748
granulocyte monocyte progenitor cell1.73e-5667
myeloid lineage restricted progenitor cell1.88e-5366
classical monocyte1.12e-4942
CD14-positive, CD16-negative classical monocyte1.12e-4942
leukocyte2.84e-42136
myeloid cell1.39e-41108
common myeloid progenitor1.39e-41108
nongranular leukocyte1.74e-34115
hematopoietic lineage restricted progenitor cell1.37e-31120
hematopoietic stem cell6.35e-31168
angioblastic mesenchymal cell6.35e-31168
hematopoietic cell5.75e-28177
hematopoietic oligopotent progenitor cell6.07e-28161
hematopoietic multipotent progenitor cell6.07e-28161
stuff accumulating cell3.03e-2487
intermediate monocyte6.56e-129
CD14-positive, CD16-positive monocyte6.56e-129
granulocyte2.49e-118
macrophage1.39e-086
immature conventional dendritic cell3.87e-085
common dendritic progenitor3.87e-085
blood cell1.26e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.43e-5998
blood island2.43e-5998
hemolymphoid system1.36e-54108
bone marrow3.25e-4776
immune system2.63e-4393
bone element3.53e-4282
skeletal element1.57e-3690
adult organism1.82e-34114
skeletal system4.93e-32100
lateral plate mesoderm4.74e-22203
musculoskeletal system4.21e-15167
blood1.13e-1115
haemolymphatic fluid1.13e-1115
organism substance1.13e-1115
mesoderm3.81e-11315
mesoderm-derived structure3.81e-11315
presumptive mesoderm3.81e-11315
neural tube2.22e-0856
neural rod2.22e-0856
future spinal cord2.22e-0856
neural keel2.22e-0856
tissue8.71e-08773
germ layer1.10e-07560
germ layer / neural crest1.10e-07560
embryonic tissue1.10e-07560
presumptive structure1.10e-07560
germ layer / neural crest derived structure1.10e-07560
epiblast (generic)1.10e-07560
embryonic structure2.15e-07564
regional part of nervous system5.45e-0753
regional part of brain5.45e-0753
telencephalon5.98e-0734
developing anatomical structure7.68e-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
NFE2#4778211.02918009308990.01376231735648680.0484452682056733
SPI1#668874.102161754261360.0006255544805661120.005149545550236



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.