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Coexpression cluster:C4783: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4783_CD14_CD19_breast_Burkitt_chronic_Mast_gall
|id=C4783
}}

Latest revision as of 14:19, 17 September 2013


Full id: C4783_CD14_CD19_breast_Burkitt_chronic_Mast_gall



Phase1 CAGE Peaks

Hg19::chr8:96146053..96146079,+p4@PLEKHF2
Hg19::chr8:96146086..96146125,+p3@PLEKHF2
Hg19::chr8:96146132..96146155,+p2@PLEKHF2


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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell1.13e-46168
angioblastic mesenchymal cell1.13e-46168
hematopoietic oligopotent progenitor cell4.07e-44161
hematopoietic multipotent progenitor cell4.07e-44161
hematopoietic cell4.20e-41177
leukocyte9.21e-39136
myeloid cell2.57e-33108
common myeloid progenitor2.57e-33108
hematopoietic lineage restricted progenitor cell4.44e-33120
nongranular leukocyte1.58e-29115
myeloid leukocyte2.11e-2672
granulocyte monocyte progenitor cell1.03e-2367
myeloid lineage restricted progenitor cell1.14e-2366
macrophage dendritic cell progenitor2.98e-2061
monopoietic cell1.23e-1959
monocyte1.23e-1959
monoblast1.23e-1959
promonocyte1.23e-1959
defensive cell1.86e-1748
phagocyte1.86e-1748
classical monocyte1.36e-1442
CD14-positive, CD16-negative classical monocyte1.36e-1442
lymphocyte of B lineage8.64e-1224
pro-B cell8.64e-1224
nucleate cell1.04e-1055
lymphocyte7.15e-1053
common lymphoid progenitor7.15e-1053
B cell1.39e-0914
lymphoid lineage restricted progenitor cell1.78e-0952
endo-epithelial cell2.18e-0742
stuff accumulating cell3.97e-0787
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.43e-2298
blood island1.43e-2298
hemolymphoid system1.21e-20108
bone marrow1.43e-1776
immune system1.37e-1693
bone element3.74e-1682
skeletal element4.98e-1490
skeletal system2.30e-10100
Disease
Ontology termp-valuen
hematologic cancer1.07e-0751
immune system cancer1.07e-0751


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)
MA0003.11.0927
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
MA0017.10.686276
MA0019.10.990656
MA0024.12.72668
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.12.26659
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.11.84783
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.12.19699
MA0101.11.55947
MA0103.10.628063
MA0105.11.5295
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.12.32521
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.12.11725
MA0146.12.3244
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.29.72073
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.05956
MA0163.12.48891
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.24.10519
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
BHLHE40#8553344.87181354697741.10603738662898e-050.000285995143902313
CCNT2#90536.336201576962630.003930750035764890.0191377373075963
CHD2#1106310.34402283411690.0009033701102746880.00663155063941647
E2F1#186934.907389214879320.008460985347239390.0328082293265142
E2F6#187635.017155731697390.00791769806886330.0324675671841852
EGR1#195834.988179094810140.008056488137383440.0322788032600679
FOXA1#3169311.08141974938550.000734755275698670.00584663666580521
GATA1#2623313.56030814380040.0004009615963782630.00389725715813396
GATA3#2625327.2365163572064.94721007899563e-050.00085529162959812
GTF2F1#2962312.73966087675770.0004835525047438590.00436187079313732
HMGN3#932438.178547723350590.001827766942164210.0109336245874728
HNF4G#3174328.75342252644684.20470658818262e-050.000761066466833977
IRF1#365937.63716375356390.002244692747297240.012883083246413
JUND#372736.994663941871030.002921845042734990.0157767849456209
MAX#414936.452555509007120.003721913834265510.0187539421497011
MXI1#460139.96157162875930.001011470541259020.0072388797271672
MYC#460935.22228187160940.007020843755740150.029635837887226
NFKB1#479035.488063424193840.006049381815655430.0270969028755034
NRF1#4899312.21027944771090.0005492172401020010.00473890443977304
POU2F2#545239.106124057742520.001324165192682130.00885991982564732
SIN3A#2594235.408884726815140.006318961977991520.0278540526746067
TAF7#6879311.43306940492390.0006690181981945830.00546170496374924
TAL1#6886329.86861667744023.75103522793067e-050.000723461437063437
TCF12#6938310.63446490218640.0008313523990202070.00632378828851212
USF1#739136.361499277207960.00388404057290560.0191315056073993
USF2#7392312.99219738506960.0004558979393427810.00423381868104399



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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