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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:37, 17 September 2013


Full id: C1072_leukemia_acute_chronic_Prostate_Keratinocyte_mesothelioma_Gingival



Phase1 CAGE Peaks

Hg19::chr21:16126066..16126068,-p5@ENST00000454128
Hg19::chr21:16126160..16126176,-p1@ENST00000455253
Hg19::chr21:16135169..16135180,-p@chr21:16135169..16135180
-
Hg19::chr4:127519543..127519548,-p@chr4:127519543..127519548
-
Hg19::chr4:127656672..127656696,-p@chr4:127656672..127656696
-
Hg19::chr8:124194961..124194972,+p4@FAM83A
Hg19::chr8:124195004..124195015,+p6@FAM83A
Hg19::chr8:124195016..124195044,+p3@FAM83A


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><br>disease_data<br>

Disease
Ontology termp-valuen
chronic leukemia3.49e-608
myeloid leukemia5.05e-3431
leukemia7.02e-2739
hematologic cancer2.35e-2051
immune system cancer2.35e-2051
chronic myeloid leukemia1.84e-141
organ system cancer6.68e-07137


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)
MA0003.10.576745
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.00962431
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.12.1209
MA0046.10.90778
MA0048.10.653157
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.524515
MA0056.10
MA0057.10.0912556
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.11.3723
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.000871324
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.948525
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.054222
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.792149
MA0105.10.586268
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.11.25157
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.11.46857
MA0140.15.63072
MA0141.11.68422
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.830366
MA0146.10.0399277
MA0147.10.243042
MA0148.11.20731
MA0149.10.506665
MA0062.20.161302
MA0035.22.21238
MA0039.20.00133745
MA0138.20.653421
MA0002.20.179788
MA0137.20.86081
MA0104.20.189646
MA0047.21.43258
MA0112.22.2406
MA0065.20.0631316
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.577214
MA0155.10.0535085
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.682702
MA0160.10.495355
MA0161.10
MA0162.10.0163939
MA0163.10.0104024
MA0164.11.51849
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.000390427
MA0102.23.22015
MA0258.11.7796
MA0259.10.699589
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
CCNT2#90575.54417637984231.68072647241023e-050.000387149078191558
CEBPB#105154.981967266140510.001250523778793020.00840650443700851
EP300#203375.92719901044531.06380393527283e-050.000276168578662589
GATA1#2623610.17023110785033.94864064622967e-060.000127675566703276
GATA2#2624711.15181526685971.36229982264474e-077.74087220768196e-06
GATA3#2625310.21369363395230.002410870126189130.0135911079082946
HDAC2#306658.384762647891410.000106287309381870.00148125704624141
HEY1#2346263.030083282329280.004001723466483270.0191872186721167
HMGN3#932477.156229257931772.91658210831366e-060.000100067318925812
JUN#372569.384621894252256.3249395698254e-060.000186707282004804
JUNB#3726519.13164541238821.91526005463182e-067.04571485895361e-05
JUND#372776.120330949137158.53888173818505e-060.000232116676172386
MXI1#460156.225982267974560.0004393954903539430.00409439914499246
SMARCA4#6597597.978689567435.77233124266155e-105.55116484946897e-08
SMARCB1#659836.844768417934030.007473690134633950.0308247659731078
SMARCC1#6599316.37375974486180.0006166336580522750.0051119703614321
SMARCC2#6601335.30826541008666.43686411657099e-050.00104713341350554
SMC3#912647.522466422466420.001098483328037180.00767285314987128
STAT1#6772512.94161718574951.29944539079553e-050.000317977453536302
STAT2#6773648.94782838983053.51075876587426e-103.51543753354882e-08
TAL1#6886726.13503959276023.64973064517802e-103.64063246276741e-08
TBP#690873.243424351209340.0006354223620492050.00521310888217258
TFAP2A#702036.194487889891860.009861483862380290.0370489410807272



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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