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Coexpression cluster:C728: Difference between revisions

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|full_id=C728_Mast_CD14_Basophils_chorionic_immature_Monocytederived_acute
|full_id=C728_Mast_CD14_Basophils_chorionic_immature_Monocytederived_acute
|id=C728
|id=C728
|ontology_enrichment_celltype=CL:0000557!2.10e-38!71;CL:0000839!3.39e-38!70;CL:0000766!8.90e-37!76;CL:0000763!1.68e-35!112;CL:0000049!1.68e-35!112;CL:0002009!4.49e-35!65;CL:0002194!1.52e-33!63;CL:0000576!1.52e-33!63;CL:0000040!1.52e-33!63;CL:0000559!1.52e-33!63;CL:0000860!6.10e-32!45;CL:0002057!1.91e-31!42;CL:0000738!1.99e-27!140;CL:0000037!1.04e-26!172;CL:0000566!1.04e-26!172;CL:0002032!3.61e-26!165;CL:0000837!3.61e-26!165;CL:0002031!1.54e-25!124;CL:0000988!1.48e-23!182;CL:0002087!2.05e-21!119;CL:0000134!1.69e-14!358;CL:0002320!2.98e-13!365;CL:0000219!7.92e-13!390;CL:0000048!2.69e-11!430;CL:0000723!1.98e-10!436;CL:0000034!2.14e-10!444
|ontology_enrichment_celltype=CL:0000860!1.33e-118!42;CL:0002057!1.33e-118!42;CL:0000473!4.83e-103!48;CL:0000234!4.83e-103!48;CL:0000839!9.28e-94!66;CL:0000557!2.73e-92!67;CL:0000766!9.47e-91!72;CL:0002194!3.00e-81!59;CL:0000576!3.00e-81!59;CL:0000040!3.00e-81!59;CL:0000559!3.00e-81!59;CL:0002009!1.95e-78!61;CL:0000763!1.01e-58!108;CL:0000049!1.01e-58!108;CL:0000325!3.56e-54!87;CL:0002031!3.87e-49!120;CL:0000738!3.18e-48!136;CL:0002087!6.84e-42!115;CL:0000037!6.90e-38!168;CL:0000566!6.90e-38!168;CL:0002032!1.95e-37!161;CL:0000837!1.95e-37!161;CL:0000988!1.20e-35!177;CL:0002274!2.54e-18!5;CL:0000457!2.54e-18!5;CL:0002191!2.54e-18!5;CL:0000097!2.54e-18!5;CL:0000831!2.54e-18!5;CL:0002028!2.54e-18!5;CL:0000134!1.33e-14!354;CL:0002320!3.44e-14!361;CL:0000219!9.76e-13!386;CL:0000048!5.87e-11!427;CL:0000723!1.03e-10!433;CL:0000034!2.15e-10!441;CL:0000163!3.13e-10!9
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002371!5.36e-36!80;UBERON:0001474!1.69e-34!86;UBERON:0002390!7.87e-31!102;UBERON:0003061!7.87e-31!102;UBERON:0002405!1.17e-29!115;UBERON:0004765!4.70e-29!101;UBERON:0001434!4.70e-29!101;UBERON:0002193!5.26e-28!112;UBERON:0002204!3.97e-14!167;UBERON:0003081!4.89e-14!216;UBERON:0002384!2.18e-12!375
|ontology_enrichment_uberon=UBERON:0002371!8.79e-81!76;UBERON:0001474!1.70e-74!82;UBERON:0004765!2.11e-67!90;UBERON:0002390!3.38e-65!98;UBERON:0003061!3.38e-65!98;UBERON:0002405!4.73e-65!93;UBERON:0001434!4.13e-60!100;UBERON:0002193!1.22e-58!108;UBERON:0002204!1.29e-33!167;UBERON:0003081!2.31e-28!203;UBERON:0000926!5.54e-16!315;UBERON:0004120!5.54e-16!315;UBERON:0006603!5.54e-16!315;UBERON:0002384!1.26e-13!371
|tf_chipseq_enrich=CCNT2#905;6:3.45610995107053:0.00346892417326783:0.0176220133144569!FOS#2353;5:4.08997968586109:0.00439067875231433:0.0208094980129314!FOSL1#8061;4:14.4413017150447:0.000114963486608592:0.0015725830488428!HMGN3#9324;6:4.4610260309185:0.000889703240209133:0.00662812730609898!HSF1#3297;3:44.8065454545455:3.57812328587162e-05:0.0006929271608625!JUN#3725;5:5.68764963288015:0.000997758818135818:0.00715300200489338!JUNB#3726;5:13.9139239362823:1.45501238171169e-05:0.000346308199939808!JUND#3727;6:3.81527124102056:0.00205979469345866:0.0119545928307935!MAFF#23764;3:15.3587335881669:0.000829509269563324:0.00631206692924765!MAFK#7975;4:9.85481205011997:0.000496061340539946:0.00438606081481979!NFE2#4778;3:21.0557074504443:0.00033130345728274:0.0033750489441233!SIRT6#51548;2:27.9342552709136:0.0022390920374544:0.012860833377314
|tf_chipseq_enrich=CCNT2#905;6:3.45610995107053:0.00346892417326783:0.0176220133144569!FOS#2353;5:4.08997968586109:0.00439067875231433:0.0208094980129314!FOSL1#8061;4:14.4413017150447:0.000114963486608592:0.0015725830488428!HMGN3#9324;6:4.4610260309185:0.000889703240209133:0.00662812730609898!HSF1#3297;3:44.8065454545455:3.57812328587162e-05:0.0006929271608625!JUN#3725;5:5.68764963288015:0.000997758818135818:0.00715300200489338!JUNB#3726;5:13.9139239362823:1.45501238171169e-05:0.000346308199939808!JUND#3727;6:3.81527124102056:0.00205979469345866:0.0119545928307935!MAFF#23764;3:15.3587335881669:0.000829509269563324:0.00631206692924765!MAFK#7975;4:9.85481205011997:0.000496061340539946:0.00438606081481979!NFE2#4778;3:21.0557074504443:0.00033130345728274:0.0033750489441233!SIRT6#51548;2:27.9342552709136:0.0022390920374544:0.012860833377314
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4803,0.120932,0.135307,0.659642,0.49569,0.560857,0.167908,0.505898,0.816691,0.116017,0.46615,0.597049,0.137272,0.201882,0.321342,0.0128495,0.0677255,0.069039,0.305067,0.100939,0.946206,0.43591,0.135223,0.285057,0.187413,0.4347,0.29105,0.592319,0.538309,0.402629,0.114719,0.629279,0.710696,0.251974,0.50054,0.268916,0.522767,0.776021,0.443444,0.428369,0.488883,0.426313,0.289378,0.742922,0.129502,0.162791,0.0525549,0.0231607,0.407148,0.0359488,0.0092739,0.0915964,0.0953267,0.925902,0.372971,0.17731,0.318785,0.171564,0.208652,0.0342832,0.302707,0.434718,0.119189,0.0331516,0.695697,0.957334,0.979863,0.592704,0.356157,0.372151,0.543363,0.512553,0.945549,0.195403,0.163718,0.839641,0.205682,0.506771,0.730433,0.237617,0.067764,0.134127,0.124403,0.388692,0.506277,0.976944,0.936432,0.571685,0.59446,0.343085,0.225589,0.344355,0.169548,0.308886,0.207307,0.25036,0.157465,0.348305,0.234465,0.242237,0.0242056,0.131401,0.40648,0.155356,0.183897,0.359054,0.300739,0.500395,0.334046,0.600989,0.194141,0.0764543,0.251557,0.710509,0.454553,0.548455,0.59461,0.324886,0.765993,0.154556,0.783196,0.452722,0.211264,0.183569,0.445539,0.727822,0.462646,0.239328,0.297755,0.203718,0.112581,0.121448,0.313173,0.460799,0.495664,0.187338,0.417939,0.61307,0.654239,0.353923,0.371665,0.274764,0.185244,0.0102617,0.354821,0.176004,0.505578,0.306067,0.675126,0.282697,0.426094,0.319827,0.298102,0.330545,0.0725749,0.0905574,0.146815,0.29423,0.960411,0.14539,0.535384,0.267489,0.52756,0.463673,0.0504432,0.92789,0.200162,0.647172,0.000105176,0.594531,0.618426,0.85307,0.971186,0.126073,0.579811,0.40264,0.150341,0.408977,0.862706,0.815459,0.373436,0.57144,0.619107,0.550684,0.00620666,0.816305,0.869563,0.641527,0.553662,0.0404952,0.80693,0.0448977,0.102233,0.00170221,0.015617,0.61371,0.990868,0.541499,0.70339,0.252256,0.170313,0.0578201,0.878604,0.995366,0.243861,0.134193,0.970611,0.107328,0.347521,0.728062,0.94733,0.991683,0.713781,0.481939,0.000133175,0.00897568,0.00501901,0.688253,0.777522,0.901445,0.66554,0.885729,0.640351,0.643714,0.542579,0.954858,0.791735,0.476008,0.883548,0.183676,0.71527,0.699444,0.511387,0.66352,0.093267,0.490916,0.878568,0.629992,0.565648,0.0504083,0.569953,0.376874,0.296226,0.603444,0.00561097,0.104301,0.463307,0.428013,0.857261,0.309722,0.402709,0.0240509,0.481099,0.61753,0.0811478,0.00844788,0.0125738,0.402693,0.520009,0.0351893,0.650495,0.277034,0.854096,0.0193191,0.417126,6.08957e-05,0.781361,0.453731,0.535996,0.753361,0.997371,0.536766,0.601724,0.861382,0.861095,0.897492,0.992274,0.102677,0.205775,0.0733958,0.422014,0.915758,0.00493191,0.554368,0.273305,0.0140577,0.692064,0.506508,0.773368,0.820016,0.0212653,0.574038,0.00732817,0.0655992,0.542413,0.808854,0.627335,0.56578,0.689958,0.250176,0.369089,0.795167,0.0321357,0.717955,0.737831,0.636412,0.50749,0.152869,0.149217,0.918851,0.534679,0.481861,0.653388,0.830046,0.65627,0.00505823,0.0648658,0.483731,0.552624,0.00831644,0.0819965,0.96585,0.389534,0.392661,0.705416,0.585772,0.904463,0.557778,0.0312629,0.814196,0.116117,0.531205,0.907755,0.485338,0.0684405,0.00939575,0.4494,0.535628,0.436682,0.00218863,0.375731,0.975006,0.56962,0.509116,0.257235,0.695354,0.20658,0.118164,0.537498,0.0992571,0.534569,0.239417,0.00603242,0.478226,0.0442218,0.139529,0.596806,0.574762,0.292558,0.307527,0.14412,0.655454,0.520027,0.294339,0.573809,0.175433,0.0372567,0.0458514,0.599595,0.0147323,0.784093,0.744402,0.594113,0.195472,0.531493,0.382823,0.196882,0.114406,0.301747,0.384693,0.51672,0.610721,0.698203,0.27961,0.402705,0.575463,0.647625,0.23559,0.225542,0.211908,0.679099,0.355997,0.438647,0.615425,0.138174,0.614558,0.492207,0.134057,0.22178,0.178456,0.157134,0.0294037,0.562004,0.212024,0.46059,0.374709,0.316768,0.343584,0.201618,0.0615366,0.468824,0.598491,0.0468982,0.0860835,0.66787,0.740651,0.518267,0.472069,0.297552,0.450676,0.592401,0.384353,0.526219,0.0407166,0.240646,0.665997,0.671331,0.566369,0.586083,0.573867,0.429354,0.544513,0.650216,0.363633,0.606456,0.645073,0.501724,0.559644,0.424261,0.552902,0.635262,0.464149,0.402607,0.663459,0.603153,0.49975,0.509988,0.311923,0.563078,0.744036,0.340739,0.594401,0.269963,0.0101816,0.338919,0.182919,0.183452,0.451616,0.257575,0.141393,0.183331,0.412879,0.102135,0.216743,0.042168,0.00330001,0.537287,0.267192,0.315214,0.215792,0.379171,0.214946,0.333105,0.222472,0.252354,0.396678,0.345496,0.152456,0.224382,0.291235,0.128266,0.412357,0.567591,0.368106,0.129023,0.0737773,0.429017,0.673635,0.661783,0.558985,0.611867,0.0430237,0.00488798,0.511893,0.125571,0.310473,0.404324,0.473851,0.571258,0.557233,0.71055,0.260286,0.763537,0.363221,0.0023651,0.238174,0.0108218,0.000178606,0.183016,0.342181,0.344927,0.090616,0.482941,0.0680729,0.302498,0.427147,0.241509,0.574325,0.30896,0.280668,0.75272,0.498751,0.469676,0.686624,0.236983,0.0301569,0.323272,0.602683,0.508119,0.466029,0.0613651,0.289432,0.570694,0.0850818
}}
}}

Revision as of 16:38, 19 October 2012


Full id: C728_Mast_CD14_Basophils_chorionic_immature_Monocytederived_acute



Phase1 CAGE Peaks

Hg19::chr10:80732616..80732631,+p@chr10:80732616..80732631
+
Hg19::chr10:80732642..80732657,+p@chr10:80732642..80732657
+
Hg19::chr10:80732663..80732675,+p@chr10:80732663..80732675
+
Hg19::chr14:35837883..35837893,-p@chr14:35837883..35837893
-
Hg19::chr16:28995941..28995949,-p5@CU678918
Hg19::chr16:28995973..28995989,-p2@CU678918
Hg19::chr18:2894355..2894361,-p@chr18:2894355..2894361
-
Hg19::chr2:63605711..63605712,+p@chr2:63605711..63605712
+
Hg19::chr4:158234555..158234556,+p@chr4:158234555..158234556
+
Hg19::chr4:87928626..87928670,-p@chr4:87928626..87928670
-
Hg19::chr8:102064237..102064245,+p1@FLJ42969


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
classical monocyte1.33e-11842
CD14-positive, CD16-negative classical monocyte1.33e-11842
defensive cell4.83e-10348
phagocyte4.83e-10348
myeloid lineage restricted progenitor cell9.28e-9466
granulocyte monocyte progenitor cell2.73e-9267
myeloid leukocyte9.47e-9172
monopoietic cell3.00e-8159
monocyte3.00e-8159
monoblast3.00e-8159
promonocyte3.00e-8159
macrophage dendritic cell progenitor1.95e-7861
myeloid cell1.01e-58108
common myeloid progenitor1.01e-58108
stuff accumulating cell3.56e-5487
hematopoietic lineage restricted progenitor cell3.87e-49120
leukocyte3.18e-48136
nongranular leukocyte6.84e-42115
hematopoietic stem cell6.90e-38168
angioblastic mesenchymal cell6.90e-38168
hematopoietic oligopotent progenitor cell1.95e-37161
hematopoietic multipotent progenitor cell1.95e-37161
hematopoietic cell1.20e-35177
histamine secreting cell2.54e-185
biogenic amine secreting cell2.54e-185
granulocytopoietic cell2.54e-185
mast cell2.54e-185
mast cell progenitor2.54e-185
basophil mast progenitor cell2.54e-185
mesenchymal cell1.33e-14354
connective tissue cell3.44e-14361
motile cell9.76e-13386
multi fate stem cell5.87e-11427
somatic stem cell1.03e-10433
stem cell2.15e-10441
endocrine cell3.13e-109
Uber Anatomy
Ontology termp-valuen
bone marrow8.79e-8176
bone element1.70e-7482
skeletal element2.11e-6790
hematopoietic system3.38e-6598
blood island3.38e-6598
immune system4.73e-6593
skeletal system4.13e-60100
hemolymphoid system1.22e-58108
musculoskeletal system1.29e-33167
lateral plate mesoderm2.31e-28203
mesoderm5.54e-16315
mesoderm-derived structure5.54e-16315
presumptive mesoderm5.54e-16315
connective tissue1.26e-13371


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
CCNT2#90563.456109951070530.003468924173267830.0176220133144569
FOS#235354.089979685861090.004390678752314330.0208094980129314
FOSL1#8061414.44130171504470.0001149634866085920.0015725830488428
HMGN3#932464.46102603091850.0008897032402091330.00662812730609898
HSF1#3297344.80654545454553.57812328587162e-050.0006929271608625
JUN#372555.687649632880150.0009977588181358180.00715300200489338
JUNB#3726513.91392393628231.45501238171169e-050.000346308199939808
JUND#372763.815271241020560.002059794693458660.0119545928307935
MAFF#23764315.35873358816690.0008295092695633240.00631206692924765
MAFK#797549.854812050119970.0004960613405399460.00438606081481979
NFE2#4778321.05570745044430.000331303457282740.0033750489441233
SIRT6#51548227.93425527091360.00223909203745440.012860833377314



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.