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Coexpression cluster:C741: Difference between revisions

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|tf_chipseq_enrich=EBF1#1879;5:4.04839402116773:0.00459238325242163:0.0217034216253976!FOS#2353;7:5.72597156020553:4.5912826243232e-05:0.000806982440258651!JUN#3725;6:6.82517955945618:8.44439089932034e-05:0.00126694977896009!NFKB1#4790;6:2.99348914046936:0.00728556496302957:0.0301405077906059!SMARCC2#6601;2:17.1191589867087:0.00581844647605355:0.0261533346895871!STAT3#6774;5:4.78157499870647:0.00219206266137762:0.0126358777067898!TBP#6908;7:2.35885407360679:0.011797348605664:0.0429783483684576
|tf_chipseq_enrich=EBF1#1879;5:4.04839402116773:0.00459238325242163:0.0217034216253976!FOS#2353;7:5.72597156020553:4.5912826243232e-05:0.000806982440258651!JUN#3725;6:6.82517955945618:8.44439089932034e-05:0.00126694977896009!NFKB1#4790;6:2.99348914046936:0.00728556496302957:0.0301405077906059!SMARCC2#6601;2:17.1191589867087:0.00581844647605355:0.0261533346895871!STAT3#6774;5:4.78157499870647:0.00219206266137762:0.0126358777067898!TBP#6908;7:2.35885407360679:0.011797348605664:0.0429783483684576
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92819,0.150458,0.560857,0.167908,0.505898,0.816691,0.116017,0.792481,0.597049,0.137272,0.201882,0.86367,0.380631,0.344691,0.000989973,0.670834,0.100939,0.946206,0.112945,0.135223,0.285057,0.187413,0.4347,0.657997,0.226519,0.0436001,0.0948532,0.840699,0.0788918,0.351879,0.0348088,0.50054,0.268916,0.169734,0.776021,0.443444,0.428369,0.488883,0.426313,0.289378,0.742922,0.710877,0.162791,0.306168,0.636157,0.407148,0.255865,0.345558,0.0147374,0.403546,0.925902,0.887401,0.17731,0.0572822,0.171564,0.208652,0.250155,0.000528624,0.112264,0.119189,0.246188,0.333658,0.548076,0.901226,0.592704,0.356157,0.372151,0.543363,0.512553,0.945549,0.195403,0.163718,0.839641,0.205682,0.506771,0.145413,0.237617,0.605162,0.716786,0.124403,0.388692,0.506277,0.999861,0.999959,0.571685,0.59446,0.343085,0.225589,0.344355,0.169548,0.308886,0.570254,0.25036,0.157465,0.348305,0.234465,0.609431,0.457137,0.131401,0.40648,0.155356,0.183897,0.359054,0.00584874,0.153701,0.334046,0.234391,0.194141,0.624261,0.251557,0.710509,0.454553,0.548455,0.59461,0.324886,0.765993,0.501626,0.198407,0.452722,0.211264,0.183569,0.445539,0.923874,0.462646,0.239328,0.297755,0.203718,0.435273,0.450432,0.313173,0.460799,0.495664,0.045885,0.417939,0.61307,0.0920533,0.71234,0.371665,0.274764,0.185244,0.356138,0.354821,0.531143,0.505578,0.306067,0.675126,0.650129,0.426094,0.319827,0.664512,0.330545,0.355935,0.0905574,0.490328,0.29423,0.832571,0.488206,0.535384,0.267489,0.173303,0.463673,0.159394,0.738271,0.200162,0.647172,0.51347,0.594531,0.250798,0.85307,0.971186,0.126073,0.85748,0.40264,0.150341,0.408977,0.862706,0.0916821,0.887595,0.301233,0.619107,0.327144,0.356608,0.816305,0.333301,0.887416,0.193611,0.0404952,0.80693,0.851919,0.102233,0.616892,0.891307,0.0193936,0.847289,0.541499,0.444651,0.921589,0.363021,0.288879,0.981974,0.86913,0.611154,0.501568,0.469213,0.833271,0.707165,0.728062,0.564079,0.521812,0.713781,0.481939,0.663958,0.712022,0.606215,0.426336,0.443153,0.204147,0.66554,0.885729,0.640351,0.912112,0.837695,0.715858,0.413083,0.137363,0.748777,0.892177,0.245111,0.838364,0.246732,0.919767,0.907367,0.975931,0.740361,0.789151,0.203442,0.559768,0.569953,0.7303,0.66279,0.149288,0.0754067,0.83006,0.463307,0.108479,0.857261,0.309722,0.0136397,0.477215,0.481099,0.61753,0.374787,0.346811,0.805341,0.402693,0.000968372,0.343212,0.804101,0.681572,0.0461237,0.497681,0.417126,0.549534,0.781361,0.859331,0.535996,0.509109,0.981753,0.313895,0.601724,0.861382,0.586901,0.081178,0.360055,0.392105,0.568435,0.647446,0.422014,0.983495,0.488066,0.194181,0.273305,0.752172,0.221762,0.506508,0.773368,0.0954294,0.75477,0.8545,0.811368,0.939529,0.837603,0.808854,0.627335,0.203552,0.689958,0.097417,0.0692357,0.795167,0.692997,0.510037,0.0470621,0.636412,0.00805074,0.738902,0.149217,0.715049,0.534679,0.732839,0.653388,0.00967281,0.389332,0.727995,0.598324,0.265874,0.552624,0.0445229,0.197592,0.850525,0.153709,0.895388,0.705416,0.806786,0.416713,0.845937,0.689775,0.501476,0.692595,0.831373,0.687906,0.804458,0.781736,0.554317,0.857142,0.535628,0.773188,0.519832,0.375731,0.0347359,0.0538163,0.509116,0.257235,0.33325,0.569392,0.118164,0.537498,0.666588,0.178611,0.239417,0.676428,0.138801,0.540379,0.479343,0.230569,0.574762,0.292558,0.000567376,0.486305,0.0927405,0.0997452,0.66105,0.573809,0.175433,0.515687,0.00866375,0.599595,0.603486,0.453128,0.049765,0.594113,0.555962,0.531493,0.382823,0.557694,0.114406,0.301747,0.384693,0.51672,0.0702006,0.698203,0.27961,0.402705,0.211738,0.647625,0.602291,0.225542,0.211908,0.679099,0.355997,0.438647,0.615425,0.477261,0.614558,0.492207,0.134057,0.22178,0.0169654,0.0130483,0.318365,0.200418,0.212024,0.0248566,0.374709,0.316768,0.0672589,0.201618,0.22457,0.468824,0.598491,0.549025,0.0860835,0.301787,0.740651,0.518267,0.134832,0.664008,0.0230232,0.592401,0.0857138,0.1723,0.173921,0.240646,0.665997,0.30562,0.566369,0.586083,0.573867,0.429354,0.544513,0.282789,0.363633,0.0683243,0.645073,0.501724,0.559644,0.424261,0.00927204,0.635262,0.025542,0.00195082,0.0249397,0.236385,0.49975,0.00614007,0.311923,0.563078,0.744036,0.7016,0.594401,0.269963,0.562934,0.338919,0.182919,0.183452,0.451616,0.257575,0.141393,0.183331,0.412879,0.305584,0.581258,0.533448,0.0758769,0.00799941,0.267192,0.315214,0.215792,0.379171,0.0249608,0.333105,0.222472,0.252354,0.0918167,0.00926835,0.152456,0.224382,0.291235,0.128266,0.0999451,0.567591,0.13961,0.351331,0.462987,0.429017,0.673635,0.661783,0.558985,0.611867,6.403e-05,0.0940159,0.0362701,0.705698,0.675667,0.404324,0.473851,0.208157,0.557233,0.12925,0.628144,0.763537,0.363221,0.228206,0.605083,0.0108218,0.0467444,0.540283,0.70279,0.705047,0.651673,0.482941,0.605877,0.302498,0.766699,0.608655,0.574325,0.30896,0.280668,0.75272,0.498751,0.133309,0.11203,0.236983,0.321769,0.323272,0.235951,0.508119,0.466029,0.224186,0.656486,0.570694,0.806913
|tfbs_overrepresentation_for_novel_motifs=0.253158,0.166992,0.246925,0.373402,0.609116,0.371921,0.44126,0.121034,0.379568,0.0713737,0.344881,0.481459,0.0905352,0.430675,0.211157,0.651838,0.650562,0.168654,0.325153,0.339956,0.246975,0.423587,0.36495,0.599268,0.779948,0.50266,0.267398,1.69684,0.214796,0.885559,0.325512,0.685875,0.14393,0.635939,0.184525,0.285028,0.182011,0.372963,0.163827,0.706689,0.183426,0.836994,0.471149,0.209923,0.183826,0.273032,0.442265,0.335245,0.711959,0.615345,0.515974,0.453148,0.403355,0.760015,0.908824,1.93816,1.16995,0.40339,0.88505,0.402472,0.725346,0.444449,0.380466,0.624068,0.461047,0.591283,0.99547,1.35949,0.675894,1.19869,0.299692,0.394628,0.176201,0.906867,0.0876634,0.973875,0.536377,0.607953,0.672773,0.280653,0.101808,0.623044,1.16527,0.123028,0.856604,0.0372554,0.0364455,0.0654897,0.540459,1.45821,1.08742,0.830286,0.702047,0.149302,0.212875,0.159241,0.0976799,0.743159,0.544807,0.455381,0.494695,0.696605,0.737766,0.654073,0.580349,0.340854,0.638916,0.427507,0.285742,0.199366,0.256397,0.735091,0.242288,0.930939,1.04009,0.533593,0.0096263,0.866759,0.58906,0.901377,0.898765,0.538171,0.369441,0.471181,1.14929,0.608677,1.11065,0.706859,0.940494,0.482616,0.830959,0.874777,0.954592,1.18111,1.10012,0.0617084,0.32024,1.69861,1.05827,1.9115,1.51034,1.02151,0.437004,0.739749,0.582016,1.02425,0.566218,1.75262,0.308276,0.146851,0.160217,0.0216333,0.831331,0.113748,0.444001,1.22899,0.525224,0.200973,0.286011,0.261307,1.02032,0.813307,0.672017,0.264042,0.597299,1.16369,1.96967,0.440034,0.0167869
}}
}}

Revision as of 14:26, 26 November 2012


Full id: C741_immature_CD14_Basophils_Peripheral_Mallassezderived_Astrocyte_renal



Phase1 CAGE Peaks

Hg19::chr11:62321495..62321531,-p@chr11:62321495..62321531
-
Hg19::chr11:62321782..62321794,+p@chr11:62321782..62321794
+
Hg19::chr14:65673392..65673400,+p@chr14:65673392..65673400
+
Hg19::chr16:85858477..85858488,+p@chr16:85858477..85858488
+
Hg19::chr16:85858491..85858507,+p@chr16:85858491..85858507
+
Hg19::chr17:29923862..29923868,-p@chr17:29923862..29923868
-
Hg19::chr20:47893707..47893719,-p@chr20:47893707..47893719
-
Hg19::chr2:27851106..27851120,+p2@GPN1
Hg19::chr3:71113123..71113139,+p@chr3:71113123..71113139
+
Hg19::chr3:71113153..71113163,+p@chr3:71113153..71113163
+
Hg19::chr6:32572606..32572629,+p@chr6:32572606..32572629
+


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 monocyte1.97e-9842
CD14-positive, CD16-negative classical monocyte1.97e-9842
defensive cell3.28e-8548
phagocyte3.28e-8548
granulocyte monocyte progenitor cell7.61e-7567
macrophage dendritic cell progenitor1.10e-7361
myeloid leukocyte2.38e-7372
myeloid lineage restricted progenitor cell7.29e-6766
monopoietic cell1.08e-6659
monocyte1.08e-6659
monoblast1.08e-6659
promonocyte1.08e-6659
leukocyte1.39e-55136
myeloid cell1.58e-55108
common myeloid progenitor1.58e-55108
stuff accumulating cell9.27e-4787
hematopoietic lineage restricted progenitor cell3.38e-46120
hematopoietic stem cell2.06e-43168
angioblastic mesenchymal cell2.06e-43168
nongranular leukocyte4.61e-43115
hematopoietic oligopotent progenitor cell5.51e-41161
hematopoietic multipotent progenitor cell5.51e-41161
hematopoietic cell8.91e-41177
intermediate monocyte2.84e-179
CD14-positive, CD16-positive monocyte2.84e-179
mesenchymal cell4.23e-17354
connective tissue cell1.36e-16361
motile cell8.21e-15386
basophil2.42e-143
natural killer cell3.16e-133
pro-NK cell3.16e-133
stem cell7.40e-13441
multi fate stem cell1.25e-12427
somatic stem cell2.50e-12433
CD1a-positive Langerhans cell1.76e-102
immature CD1a-positive Langerhans cell1.76e-102
Langerhans cell1.31e-085
single nucleate cell8.76e-073
mononuclear cell8.76e-073
Uber Anatomy
Ontology termp-valuen
bone marrow3.60e-6576
bone element6.96e-6082
hematopoietic system3.09e-5598
blood island3.09e-5598
skeletal element6.41e-5490
immune system6.05e-5293
hemolymphoid system2.04e-49108
skeletal system8.61e-48100
musculoskeletal system1.54e-25167
lateral plate mesoderm1.48e-22203
connective tissue6.64e-16371
mesoderm1.27e-11315
mesoderm-derived structure1.27e-11315
presumptive mesoderm1.27e-11315


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
EBF1#187954.048394021167730.004592383252421630.0217034216253976
FOS#235375.725971560205534.5912826243232e-050.000806982440258651
JUN#372566.825179559456188.44439089932034e-050.00126694977896009
NFKB1#479062.993489140469360.007285564963029570.0301405077906059
SMARCC2#6601217.11915898670870.005818446476053550.0261533346895871
STAT3#677454.781574998706470.002192062661377620.0126358777067898
TBP#690872.358854073606790.0117973486056640.0429783483684576



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.