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Coexpression cluster:C3712: Difference between revisions

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{{Coexpression_clusters
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091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.846801,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;2.3244,MA0147.1;2.37462,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;1.15986,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;2.13189,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.711948,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;5.21222,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;5.16052,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;1.40979,MA0442.1;0}}
|full_id=C3712_granulocyte_Neutrophils_embryonic_non_Eosinophils_CD19_rectum
|id=C3712
}}

Latest revision as of 12:31, 17 September 2013


Full id: C3712_granulocyte_Neutrophils_embryonic_non_Eosinophils_CD19_rectum



Phase1 CAGE Peaks

Hg19::chr18:2655849..2655941,+p2@SMCHD1
Hg19::chr6:79787902..79787958,-p1@PHIP
Hg19::chr6:79787964..79787994,-p2@PHIP


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

GO IDGO nameFDR corrected p-value
GO:0005158insulin receptor binding0.0263626274788933
GO:0008286insulin receptor signaling pathway0.0263626274788933



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
hematopoietic stem cell3.78e-37168
angioblastic mesenchymal cell3.78e-37168
hematopoietic cell7.30e-34177
leukocyte1.12e-33136
hematopoietic oligopotent progenitor cell1.28e-33161
hematopoietic multipotent progenitor cell1.28e-33161
hematopoietic lineage restricted progenitor cell1.29e-26120
nongranular leukocyte1.05e-25115
nucleate cell3.50e-1755
lymphocyte5.24e-1753
common lymphoid progenitor5.24e-1753
lymphoid lineage restricted progenitor cell1.30e-1652
myeloid cell1.62e-16108
common myeloid progenitor1.62e-16108
myeloid leukocyte3.91e-1372
granulocyte monocyte progenitor cell3.84e-1167
myeloid lineage restricted progenitor cell2.63e-1066
T cell6.53e-1025
pro-T cell6.53e-1025
classical monocyte2.11e-0942
CD14-positive, CD16-negative classical monocyte2.11e-0942
mature alpha-beta T cell4.24e-0918
alpha-beta T cell4.24e-0918
immature T cell4.24e-0918
mature T cell4.24e-0918
immature alpha-beta T cell4.24e-0918
macrophage dendritic cell progenitor5.00e-0961
monopoietic cell1.80e-0859
monocyte1.80e-0859
monoblast1.80e-0859
promonocyte1.80e-0859
defensive cell1.51e-0748
phagocyte1.51e-0748
B cell1.99e-0714
Uber Anatomy
Ontology termp-valuen
adult organism1.37e-14114
hematopoietic system2.62e-1398
blood island2.62e-1398
hemolymphoid system9.19e-11108
nervous system1.40e-0889
central nervous system3.22e-0881
bone element8.30e-0882
neural tube8.60e-0856
neural rod8.60e-0856
future spinal cord8.60e-0856
neural keel8.60e-0856
bone marrow1.06e-0776
regional part of nervous system2.59e-0753
regional part of brain2.59e-0753
regional part of forebrain4.43e-0741
forebrain4.43e-0741
anterior neural tube4.43e-0741
future forebrain4.43e-0741
immune system5.83e-0793


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)
MA0003.13.22681
MA0004.10.826076
MA0006.11.5435
MA0007.11.88666
MA0009.11.3275
MA0014.12.44638
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
MA0041.11.97353
MA0042.11.89908
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.11.23283
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.990225
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.12.03569
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
MA0105.10.846801
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
MA0146.12.3244
MA0147.12.37462
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.15986
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.15.21222
MA0163.10.122425
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
CCNT2#90536.336201576962630.003930750035764890.01898989744589
EGR1#195834.988179094810140.008056488137383440.0320452284945039
ELF1#199734.258097958807540.01295179875054610.046193112376064
GATA1#2623313.56030814380040.0004009615963782630.00387741001519902
HDAC2#3066313.41562023662630.0004140761399857210.00391151392763827
NFKB1#479035.488063424193840.006049381815655430.026944361457064
NFYB#4801211.17319550235760.01025467135054530.0381242923672077
PBX3#5090214.60967512449610.006056122473217890.0268279341270955
POU2F2#545239.106124057742520.001324165192682130.00881755219067387
RXRA#6256213.38307809275550.007196434429465730.0298273043645913
SIN3A#2594235.408884726815140.006318961977991520.0276498269657892
TFAP2C#7022310.80922860986020.0007916746575753130.00615649363831036
TRIM28#10155212.39368336350830.008368344129438470.0329059296887961
YY1#752834.911170749853860.008441455341808260.0329121273170983



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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