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Coexpression cluster:C1760: Difference between revisions

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{{Coexpression_clusters
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|full_id=C1760_brain_occipital_temporal_duodenum_parietal_medulloblastoma_myeloma
|id=C1760
}}

Latest revision as of 11:51, 17 September 2013


Full id: C1760_brain_occipital_temporal_duodenum_parietal_medulloblastoma_myeloma



Phase1 CAGE Peaks

Hg19::chr16:28303874..28303916,+p2@SBK1
Hg19::chr1:200992739..200992763,-p3@KIF21B
Hg19::chr1:200992771..200992815,-p1@KIF21B
Hg19::chr1:200992827..200992867,-p2@KIF21B
Hg19::chr3:111393542..111393579,+p1@PLCXD2


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 cell4.70e-31177
hematopoietic stem cell2.41e-30168
angioblastic mesenchymal cell2.41e-30168
hematopoietic oligopotent progenitor cell2.74e-28161
hematopoietic multipotent progenitor cell2.74e-28161
leukocyte2.72e-24136
nongranular leukocyte8.38e-23115
lymphocyte1.15e-2253
common lymphoid progenitor1.15e-2253
lymphoid lineage restricted progenitor cell2.02e-2252
nucleate cell1.99e-2155
hematopoietic lineage restricted progenitor cell5.48e-19120
T cell3.63e-1425
pro-T cell3.63e-1425
mature alpha-beta T cell2.68e-1118
alpha-beta T cell2.68e-1118
immature T cell2.68e-1118
mature T cell2.68e-1118
immature alpha-beta T cell2.68e-1118
myeloid cell1.99e-09108
common myeloid progenitor1.99e-09108
CD8-positive, alpha-beta T cell5.46e-0811
lymphocyte of B lineage5.51e-0824
pro-B cell5.51e-0824
Uber Anatomy
Ontology termp-valuen
central nervous system1.10e-1781
neural tube8.55e-1756
neural rod8.55e-1756
future spinal cord8.55e-1756
neural keel8.55e-1756
adult organism7.92e-16114
regional part of nervous system8.18e-1653
regional part of brain8.18e-1653
nervous system1.39e-1489
regional part of forebrain8.11e-1441
forebrain8.11e-1441
anterior neural tube8.11e-1441
future forebrain8.11e-1441
brain1.88e-1368
future brain1.88e-1368
telencephalon6.58e-1334
brain grey matter7.43e-1334
gray matter7.43e-1334
cerebral hemisphere2.12e-1232
regional part of cerebral cortex2.12e-1222
regional part of telencephalon3.86e-1232
neocortex1.55e-1120
cerebral cortex8.05e-1025
pallium8.05e-1025
blood3.42e-0915
haemolymphatic fluid3.42e-0915
organism substance3.42e-0915
neural plate6.77e-0982
presumptive neural plate6.77e-0982
pre-chordal neural plate2.01e-0861
neurectoderm2.64e-0886
hemolymphoid system3.49e-08108
hematopoietic system5.17e-0898
blood island5.17e-0898
Disease
Ontology termp-valuen
hematologic cancer1.00e-1051
immune system cancer1.00e-1051
leukemia3.83e-0839


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)
MA0003.19.12042
MA0004.10.626788
MA0006.11.14863
MA0007.12.50943
MA0009.11.11255
MA0014.11.02528
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.554727
MA0058.10.523638
MA0059.11.29682
MA0060.13.25531
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.11.98392
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.143.9929
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.13.31872
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.14.34317
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.12.96863
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.12.01656
MA0146.14.84512
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.777733
MA0035.20.691506
MA0039.210.268
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.20.136971
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.514087
MA0155.15.79564
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.12.27598
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.213.0494
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
E2F1#186954.907389214879320.0003512818099256460.00352696798181355
E2F6#187644.013724585357910.006632118233933880.0282934437414248
EGR1#195854.988179094810140.0003237398000590710.00330702865594379
ETS1#211335.83725655332140.009253279045631430.0349715281988384
MYC#460944.177825497287520.005691969036823440.0256787712413306
SIN3A#2594244.327107781452110.004977052855762880.0232436803292501
SRF#672238.278306957300690.003404846073776150.0173606756382906



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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