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{{Coexpression_clusters
{
|full_id=C3220_Dendritic_Burkitt_thymus_CD4_CD34_lymphoma_CD8
 

Latest revision as of 12:21, 17 September 2013


Full id: C3220_Dendritic_Burkitt_thymus_CD4_CD34_lymphoma_CD8



Phase1 CAGE Peaks

Hg19::chr12:104323463..104323474,-p@chr12:104323463..104323474
-
Hg19::chr12:110434021..110434034,-p7@GIT2
Hg19::chr12:110434043..110434066,-p3@GIT2


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 cell7.38e-47168
angioblastic mesenchymal cell7.38e-47168
hematopoietic cell5.85e-45177
leukocyte5.12e-43136
hematopoietic oligopotent progenitor cell1.65e-41161
hematopoietic multipotent progenitor cell1.65e-41161
nongranular leukocyte5.59e-35115
lymphocyte9.24e-3553
common lymphoid progenitor9.24e-3553
lymphoid lineage restricted progenitor cell6.59e-3452
hematopoietic lineage restricted progenitor cell7.98e-34120
nucleate cell1.46e-3255
lymphocyte of B lineage1.03e-1624
pro-B cell1.03e-1624
T cell1.07e-1525
pro-T cell1.07e-1525
mature alpha-beta T cell1.94e-1418
alpha-beta T cell1.94e-1418
immature T cell1.94e-1418
mature T cell1.94e-1418
immature alpha-beta T cell1.94e-1418
myeloid cell1.41e-12108
common myeloid progenitor1.41e-12108
B cell1.09e-1114
myeloid leukocyte1.08e-0972
CD8-positive, alpha-beta T cell4.02e-0911
granulocyte monocyte progenitor cell4.98e-0867
mesenchymal cell5.92e-08354
connective tissue cell4.27e-07361
motile cell5.40e-07386
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.31e-1598
blood island7.31e-1598
hemolymphoid system3.52e-12108
immune system8.59e-0893
blood3.17e-0715
haemolymphatic fluid3.17e-0715
organism substance3.17e-0715
bone marrow4.37e-0776
Disease
Ontology termp-valuen
hematologic cancer1.23e-0951
immune system cancer1.23e-0951
lymphoma3.35e-0710


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
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
MA0048.13.37768
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
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
MA0073.13.33427
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
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
MA0141.11.6959
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.22.07067
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.69213
MA0102.21.88331
MA0258.12.22591
MA0259.11.40979
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#467214.97544968400580.005768294540793880.0259468909271243
BCLAF1#9774321.65264761012189.8473954032885e-050.00138904933620212
ELF1#199734.258097958807540.01295179875054610.046035902042279
ELK4#2005210.8237877723120.01091284719516480.040176496341505
ETS1#211339.728760922202340.001085840092584840.00760437560715267
GABPB1#255337.067683836182170.002832212825417420.0153682898775794
MAX#414936.452555509007120.003721913834265510.018589811522566
MYC#460935.22228187160940.007020843755740150.0293393846433157
NFKB1#479035.488063424193840.006049381815655430.0268721614327437
SIN3A#2594235.408884726815140.006318961977991520.0275643668039202
SIX5#147912317.0867153554590.0002004060546325010.00239120392319933
TFAP2C#7022310.80922860986020.0007916746575753130.00613365797941455
THAP1#55145220.91276306856750.002983447413736940.0158617524151533
YY1#752834.911170749853860.008441455341808260.0328165700518561
ZBTB7A#5134137.35190930787590.002516255860282270.0139710391170664



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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