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Coexpression cluster:C1181: Difference between revisions

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{{Coexpression_clusters
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69,0.416144,0.648861|tfbs_overrepresentation_for_novel_motifs=0.392069,0.465735,3.64212,0.529489,0.343148,0.52784,0.604235,0.226729,0.224331,2.19177,0.497563,0.647852,4.80111,1.44576,0.341795,0.365029,0.827563,0.28906,0.19568,1.10853,0.384762,0.85713,0.520063,0.338096,0.430372,2.71467,0.957451,0.517892,0.915262,0.898182,1.1974,0.864517,2.83783,0.186138,0.309012,1.89523,8.48977,1.3112,0.282922,2.49588,0.307642,5.23567,1.38248,0.340293,0.794027,0.415364,2.50499,2.11685,0.237549,0.346342,0.684981,0.617179,0.373994,0.941629,1.09491,1.45196,0.350547,0.562713,0.150585,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,1.13397,0.232216,16.8826,1.0929,1.01827,0.971313,0.156354,0.782748,0.850825,0.424224,0.200147,0.798651,0.625403,0.229431,1.04131,8.48357,1.10085,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.910085,0.277058,0.194299,0.924148,0.715799,2.59259,0.28424,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,0.327379,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,1.90797,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,4.22331,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.26104,1.70162,13.4938,1.0153,1.16378,0.607223,1.42052,0.694887,0.329354,0.430431,3.74372,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.24928,0.602897,0.033943|tfbs_overrepresentation_jaspar=MA0003.1;6.67348,MA0004.1;1.25543,MA0006.1;0.341337,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;1.67472,MA0017.1;0.380797,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;0.35747,MA0029.1;0.886702,MA0030.1;0.875089,MA0031.1;0.809638,MA0038.1;0.60704,MA0040.1;0.892629,MA0041.1;0.521615,MA0042.1;0.48922,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;10.4132,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;6.55565,MA0056.1;0,MA0057.1;0.115382,MA0058.1;1.84591,MA0059.1;0.404929,MA0060.1;0.224688,MA0061.1;0.198335,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;0.162298,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;0.336328,MA0074.1;0.60198,MA0076.1;0.422297,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;0.405093,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;0.917255,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;2.05178,MA0093.1;2.46783,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.347695,MA0103.1;0.332048,MA0105.1;0.104569,MA0106.1;0.648997,MA0107.1;0.274127,MA0108.2;0.806528,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;0.269076,MA0115.1;1.21667,MA0116.1;0.277571,MA0117.1;1.01134,MA0119.1;0.388712,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,MA0130.1;0,MA0131.1;0.722072,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;0.614215,MA0139.1;4.83217,MA0140.1;0.564957,MA0141.1;0.403171,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.254954,MA0145.1;0.581146,MA0146.1;1.54462,MA0147.1;0.768766,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;0.564239,MA0039.2;3.59026,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;0.36398,MA0104.2;0.223944,MA0047.2;0.636643,MA0112.2;0.262665,MA0065.2;0.0828768,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.102476,MA0155.1;4.54415,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;2.53048,MA0163.1;1.72058,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;2.98307,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;0.289405,MA0442.1;0}}
|full_id=C1181_Myoblast_CD14_liposarcoma_mesenchymal_caudate_diencephalon_putamen
|id=C1181
}}

Latest revision as of 11:39, 17 September 2013


Full id: C1181_Myoblast_CD14_liposarcoma_mesenchymal_caudate_diencephalon_putamen



Phase1 CAGE Peaks

Hg19::chr12:90102690..90102701,-p13@ATP2B1
Hg19::chr12:90102773..90102784,-p6@ATP2B1
Hg19::chr12:90102800..90102814,-p4@ATP2B1
Hg19::chr12:90102818..90102829,-p10@ATP2B1
Hg19::chr12:90102935..90102948,-p5@ATP2B1
Hg19::chr12:90102960..90102971,-p7@ATP2B1
Hg19::chr12:90102986..90102998,-p12@ATP2B1


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 monocyte6.38e-2642
CD14-positive, CD16-negative classical monocyte6.38e-2642
leukocyte8.04e-23136
defensive cell5.42e-2148
phagocyte5.42e-2148
nongranular leukocyte7.27e-20115
myeloid leukocyte2.51e-1972
macrophage dendritic cell progenitor2.80e-1861
hematopoietic lineage restricted progenitor cell6.23e-18120
monopoietic cell1.45e-1759
monocyte1.45e-1759
monoblast1.45e-1759
promonocyte1.45e-1759
granulocyte monocyte progenitor cell1.55e-1767
myeloid lineage restricted progenitor cell3.40e-1566
hematopoietic stem cell1.57e-14168
angioblastic mesenchymal cell1.57e-14168
hematopoietic oligopotent progenitor cell1.10e-13161
hematopoietic multipotent progenitor cell1.10e-13161
hematopoietic cell1.29e-12177
myeloid cell2.08e-10108
common myeloid progenitor2.08e-10108
connective tissue cell7.87e-09361
mesenchymal cell8.37e-09354
multi fate stem cell6.32e-08427
stem cell1.56e-07441
somatic stem cell2.89e-07433
motile cell6.34e-07386
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.71e-1598
blood island4.71e-1598
bone marrow5.70e-1576
cerebral hemisphere1.48e-1432
regional part of forebrain9.23e-1441
forebrain9.23e-1441
anterior neural tube9.23e-1441
future forebrain9.23e-1441
telencephalon1.57e-1334
regional part of telencephalon8.53e-1332
brain grey matter1.96e-1234
gray matter1.96e-1234
regional part of cerebral cortex2.01e-1222
bone element2.51e-1282
immune system9.39e-1293
skeletal system1.39e-11100
hemolymphoid system1.68e-11108
neocortex2.24e-1120
skeletal element2.65e-1190
regional part of nervous system8.34e-1153
regional part of brain8.34e-1153
cerebral cortex1.24e-1025
pallium1.24e-1025
neural tube3.23e-1056
neural rod3.23e-1056
future spinal cord3.23e-1056
neural keel3.23e-1056
central nervous system1.83e-0981
connective tissue2.22e-09371
nervous system3.15e-0989
brain3.36e-0968
future brain3.36e-0968
musculoskeletal system4.21e-07167


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)
MA0003.16.67348
MA0004.11.25543
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.11.67472
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.110.4132
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.16.55565
MA0056.10
MA0057.10.115382
MA0058.11.84591
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.336328
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.917255
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.12.05178
MA0093.12.46783
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.14.83217
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.581146
MA0146.11.54462
MA0147.10.768766
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.23.59026
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.262665
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.14.54415
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.12.53048
MA0163.11.72058
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.22.98307
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
MA0442.10



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
ATF3#467619.25414959372185.23155102976118e-083.33360560095929e-06
BHLHE40#8553744.87181354697742.71655591272133e-123.64203315749298e-10
CCNT2#90576.336201576962632.43743907326287e-068.61759307286733e-05
CHD2#1106710.34402283411697.88338195961115e-084.72094339724673e-06
CTCF#1066475.360256373075037.86114662284756e-060.00022237548541267
E2F1#186974.907389214879321.45832274679793e-050.000346779984865276
E2F6#187675.017155731697391.24910426162553e-050.000308113367926095
EGR1#195874.988179094810141.30079520165561e-050.000318084172478834
GATA1#262335.811560633057330.01119311600820290.0411271405425239
HDAC2#3066611.49910305996541.1228817392662e-064.62067162991419e-05
HEY1#2346274.040111043105715.68979821988558e-050.00094986706567556
JUND#372765.995426235889455.24232039014691e-050.000891262736816789
MAX#414965.530761864863258.40673768319711e-050.00126184431861946
NFKB1#479075.488063424193846.66568321176054e-060.000194674857089782
NRF1#489958.721628176936366.71450045004423e-050.00107356967621275
PAX5#507976.669565531177831.7023051190758e-066.43456548429814e-05
POLR2A#543072.147453176558070.004747636447610280.0223330512094392
SIN3A#2594275.408884726815147.3795239773719e-060.000211559183275527
TAF1#687273.343046285745290.0002142336319622450.00246522105426454
TBP#690863.177232017511190.002074112051852660.012018986216692
TFAP2C#7022710.80922860986025.79365976833206e-083.61028659036296e-06
USF1#739165.452713666178259.13505145927422e-050.00133136427484669
USF2#7392712.99219738506961.59819543071901e-081.16641462326249e-06



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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