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Coexpression cluster:C4658: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4658_Neutrophils_small_Eosinophils_CD14_neuroectodermal_Whole_Peripheral
|id=C4658
}}

Latest revision as of 14:17, 17 September 2013


Full id: C4658_Neutrophils_small_Eosinophils_CD14_neuroectodermal_Whole_Peripheral



Phase1 CAGE Peaks

Hg19::chr7:139876734..139876764,-p2@JHDM1D
Hg19::chr7:139876770..139876799,-p1@JHDM1D
Hg19::chr7:139876812..139876860,-p3@JHDM1D


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
leukocyte4.23e-35136
hematopoietic lineage restricted progenitor cell1.97e-29120
nongranular leukocyte7.54e-29115
myeloid leukocyte3.95e-2572
defensive cell6.66e-2348
phagocyte6.66e-2348
hematopoietic stem cell6.91e-23168
angioblastic mesenchymal cell6.91e-23168
macrophage dendritic cell progenitor4.30e-2261
hematopoietic oligopotent progenitor cell8.31e-22161
hematopoietic multipotent progenitor cell8.31e-22161
classical monocyte9.30e-2242
CD14-positive, CD16-negative classical monocyte9.30e-2242
myeloid lineage restricted progenitor cell1.32e-2166
hematopoietic cell2.30e-21177
monopoietic cell4.63e-2159
monocyte4.63e-2159
monoblast4.63e-2159
promonocyte4.63e-2159
granulocyte monocyte progenitor cell1.37e-2067
myeloid cell3.57e-14108
common myeloid progenitor3.57e-14108
mature alpha-beta T cell3.96e-0918
alpha-beta T cell3.96e-0918
immature T cell3.96e-0918
mature T cell3.96e-0918
immature alpha-beta T cell3.96e-0918
nucleate cell2.25e-0855
lymphoid lineage restricted progenitor cell6.22e-0852
stuff accumulating cell8.60e-0887
lymphocyte1.24e-0753
common lymphoid progenitor1.24e-0753
T cell2.93e-0725
pro-T cell2.93e-0725
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.75e-2498
blood island2.75e-2498
hemolymphoid system2.22e-21108
adult organism8.10e-21114
bone marrow4.31e-1676
immune system1.31e-1493
bone element1.75e-1482
skeletal element2.11e-1190
skeletal system2.46e-09100
blood3.13e-0915
haemolymphatic fluid3.13e-0915
organism substance3.13e-0915


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)
MA0003.12.05336
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.12.44638
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.12.67616
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
MA0048.12.45333
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.15.8296
MA0056.10
MA0057.11.59304
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
MA0073.10.0834661
MA0074.10.935474
MA0076.12.91768
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
MA0092.10.785956
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
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.14.51393
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
MA0112.20.264678
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
MA0162.15.21222
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.25.16052
MA0102.21.88331
MA0258.10.519674
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
BCLAF1#9774321.65264761012189.8473954032885e-050.00139470047263907
CCNT2#90536.336201576962630.003930750035764890.0191101202395144
E2F1#186934.907389214879320.008460985347239390.0327595776926053
E2F4#1874312.66806031528440.0004917987006298980.00438887161369614
E2F6#187635.017155731697390.00791769806886330.0324230108459071
EGR1#195834.988179094810140.008056488137383440.0322404615135332
ELF1#199734.258097958807540.01295179875054610.0464852025742563
ELK4#2005316.2356816584680.0002336043955745990.00256356094036099
EP300#203336.77394172622320.003216880500103790.0168421787923772
ETS1#211339.728760922202340.001085840092584840.00765054667944868
GABPB1#255337.067683836182170.002832212825417420.0154776555530203
GATA1#2623313.56030814380040.0004009615963782630.00389363348806596
HDAC2#3066313.41562023662630.0004140761399857210.00393464634555261
HMGN3#932438.178547723350590.001827766942164210.0109179908300554
MYC#460935.22228187160940.007020843755740150.029598752714881
NRF1#4899312.21027944771090.0005492172401020010.00473421090615821
REST#597839.650028716128020.001112636247114590.00771136883750751
SIN3A#2594235.408884726815140.006318961977991520.0278223469654071
THAP1#55145331.36914460285133.23800758564397e-050.000648962337818213
USF1#739136.361499277207960.00388404057290560.0191134765770008
YY1#752834.911170749853860.008441455341808260.0331161127805241
ZBTB7A#5134137.35190930787590.002516255860282270.0140893869714786
ZNF263#1012738.221841637010680.001799043925565870.0110102753320934



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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