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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=-0.

Latest revision as of 12:07, 17 September 2013


Full id: C2519_cerebellum_CD8_Natural_CD4_Mast_Basophils_Peripheral



Phase1 CAGE Peaks

Hg19::chr1:144533782..144533805,+p@chr1:144533782..144533805
+
Hg19::chr4:2420335..2420354,-p2@ZFYVE28
Hg19::chr4:2420357..2420413,-p1@ZFYVE28
Hg19::chr4:2420416..2420440,-p4@ZFYVE28


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
leukocyte3.41e-14136
nongranular leukocyte2.24e-12115
hematopoietic lineage restricted progenitor cell1.69e-11120
defensive cell4.48e-1148
phagocyte4.48e-1148
myeloid leukocyte5.77e-1172
granulocyte monocyte progenitor cell1.51e-1067
macrophage dendritic cell progenitor6.62e-1061
classical monocyte7.36e-1042
CD14-positive, CD16-negative classical monocyte7.36e-1042
mature alpha-beta T cell8.03e-1018
alpha-beta T cell8.03e-1018
immature T cell8.03e-1018
mature T cell8.03e-1018
immature alpha-beta T cell8.03e-1018
monopoietic cell1.53e-0959
monocyte1.53e-0959
monoblast1.53e-0959
promonocyte1.53e-0959
myeloid lineage restricted progenitor cell3.30e-0966
hematopoietic cell1.33e-08177
hematopoietic stem cell4.99e-08168
angioblastic mesenchymal cell4.99e-08168
T cell1.06e-0725
pro-T cell1.06e-0725
hematopoietic oligopotent progenitor cell2.14e-07161
hematopoietic multipotent progenitor cell2.14e-07161
Uber Anatomy
Ontology termp-valuen
adult organism9.37e-29114
neural tube6.14e-2256
neural rod6.14e-2256
future spinal cord6.14e-2256
neural keel6.14e-2256
regional part of nervous system1.34e-2053
regional part of brain1.34e-2053
brain2.49e-1768
future brain2.49e-1768
regional part of forebrain3.82e-1741
forebrain3.82e-1741
anterior neural tube3.82e-1741
future forebrain3.82e-1741
neural plate5.20e-1682
presumptive neural plate5.20e-1682
central nervous system1.72e-1581
nervous system4.52e-1589
neurectoderm6.59e-1586
brain grey matter3.58e-1434
gray matter3.58e-1434
telencephalon7.11e-1434
hematopoietic system1.10e-1398
blood island1.10e-1398
hemolymphoid system1.91e-13108
cerebral hemisphere4.16e-1332
regional part of telencephalon4.35e-1332
regional part of cerebral cortex3.78e-1222
neocortex3.86e-1120
pre-chordal neural plate7.01e-1161
bone marrow1.82e-0976
cerebral cortex1.93e-0925
pallium1.93e-0925
immune system1.94e-0993
structure with developmental contribution from neural crest2.07e-09132
bone element1.31e-0882
ecto-epithelium1.17e-07104
lateral plate mesoderm1.49e-07203
tube2.75e-07192


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)
MA0003.17.59831
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.896009
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.11.92746
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.214613
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.62583
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.13.39971
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.23.66694
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.22.35508
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.57817
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.21.38179
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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#467316.84738089450660.0003409986823655640.00346435422058143
CCNT2#90546.336201576962630.0006203100587215640.00512252409447469
CHD2#110637.758017125587640.003351522464536340.0172982285482437
CTCF#1066445.360256373075030.001211145381643620.00817493779573956
E2F4#1874412.66806031528443.88145892637771e-050.00072687051965566
E2F6#187645.017155731697390.00157802193473060.00997078061838762
EBF1#187936.679850134926750.005184294118278910.0240491469049894
ELF1#199744.258097958807540.003041525565781240.0160918889850368
ESR1#2099323.07645247211590.0001339105244968570.00175807432657791
ETS1#211337.296570691651750.00400857377511390.019205956349166
HEY1#2346244.040111043105710.00375304636917980.0186117953347944
HMGN3#932448.178547723350590.0002234570284440470.00248140654903433
IRF1#365947.63716375356390.0002938853996185490.0030754606463689
MAX#414934.839416631755340.01315737137836840.0466237814062163
MXI1#460149.96157162875930.0001015224754950450.00142397338412933
PAX5#507935.002174148383370.01196533174786410.0434977647121437
RFX5#5993412.04791082719514.74457429336527e-050.000826691015390015
SIN3A#2594245.408884726815140.001168172384885160.00796466612514825
SIX5#147912312.81503651659420.0007664471136930380.0060167596292083
SMARCC2#6601370.61653082017324.74678670742709e-060.000147194078662998
SP1#666745.69838137814090.0009482606065333980.00684324139619552
SREBF1#6720447.00584944048832.04523668136926e-071.10274896110235e-05
SRF#6722413.79717826216782.75840773062708e-050.000584588768220294
USF1#739146.361499277207960.0006105011399140830.00507967882022681
ZNF143#7702310.12565741417090.001534861610688180.00976780280047915



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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