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Coexpression cluster:C1522: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;12.1731,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;1.149,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;1.85223,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;1.45353,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.0586456,MA0056.1;0,MA0057.1;0.882847,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.671725,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.199491,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.00563817,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;1.15882,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;1.61871,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;1.02896,MA0103.1;1.76074,MA0105.1;0.134725,MA0106.1;0.70837,MA0107.1;0.857383,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;0.323925,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;0.226048,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;1.16614,MA0146.1;0.718193,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;3.52102,MA0035.2;0.621793,MA0039.2;0.35955,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;1.35181,MA0047.2;0.695777,MA0112.2;0.101413,MA0065.2;0.109623,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.413181,MA0155.1;0.65596,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;11.5456,MA0163.1;0.0270301,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;1.52352,MA0079.2;0.476723,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:59, 22 January 2013


Full id: C1522_CD8_Natural_CD4_Basophils_thymus_Peripheral_CD19



Phase1 CAGE Peaks

Hg19::chr4:36245956..36245972,-p6@ARAP2
Hg19::chr4:36245985..36246005,-p3@ARAP2
Hg19::chr4:36246020..36246034,-p10@ARAP2
Hg19::chr4:36246039..36246051,-p11@ARAP2
Hg19::chr4:36246229..36246251,-p7@ARAP2
Hg19::chr5:49962495..49962577,+p1@PARP8


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:0003950NAD+ ADP-ribosyltransferase activity0.0134228187919463
GO:0016763transferase activity, transferring pentosyl groups0.0141292829388908



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
leukocyte2.54e-49136
nongranular leukocyte2.53e-40115
hematopoietic stem cell3.45e-39168
angioblastic mesenchymal cell3.45e-39168
hematopoietic lineage restricted progenitor cell5.63e-38120
hematopoietic cell5.47e-37177
hematopoietic oligopotent progenitor cell4.52e-35161
hematopoietic multipotent progenitor cell4.52e-35161
lymphocyte6.44e-2653
common lymphoid progenitor6.44e-2653
lymphoid lineage restricted progenitor cell1.19e-2552
nucleate cell4.97e-2455
myeloid leukocyte8.20e-1772
classical monocyte1.09e-1542
CD14-positive, CD16-negative classical monocyte1.09e-1542
granulocyte monocyte progenitor cell1.20e-1467
mature alpha-beta T cell1.73e-1418
alpha-beta T cell1.73e-1418
immature T cell1.73e-1418
mature T cell1.73e-1418
immature alpha-beta T cell1.73e-1418
macrophage dendritic cell progenitor4.14e-1461
defensive cell7.21e-1448
phagocyte7.21e-1448
T cell1.12e-1325
pro-T cell1.12e-1325
monopoietic cell2.96e-1359
monocyte2.96e-1359
monoblast2.96e-1359
promonocyte2.96e-1359
myeloid lineage restricted progenitor cell8.55e-1366
myeloid cell2.20e-12108
common myeloid progenitor2.20e-12108
lymphocyte of B lineage6.86e-1124
pro-B cell6.86e-1124
CD8-positive, alpha-beta T cell1.01e-0911
B cell2.96e-0914
Uber Anatomy
Ontology termp-valuen
adult organism5.16e-23114
hematopoietic system8.40e-2298
blood island8.40e-2298
hemolymphoid system1.74e-18108
neural tube4.29e-1656
neural rod4.29e-1656
future spinal cord4.29e-1656
neural keel4.29e-1656
regional part of nervous system1.16e-1453
regional part of brain1.16e-1453
regional part of forebrain1.51e-1441
forebrain1.51e-1441
anterior neural tube1.51e-1441
future forebrain1.51e-1441
telencephalon8.80e-1334
brain grey matter1.19e-1234
gray matter1.19e-1234
immune system3.37e-1293
cerebral hemisphere7.91e-1232
regional part of telencephalon9.34e-1232
bone marrow9.59e-1276
regional part of cerebral cortex1.36e-1022
brain4.33e-1068
future brain4.33e-1068
central nervous system7.31e-1081
bone element9.03e-1082
neocortex9.53e-1020
blood4.34e-0915
haemolymphatic fluid4.34e-0915
organism substance4.34e-0915
cerebral cortex8.52e-0925
pallium8.52e-0925
neural plate2.69e-0882
presumptive neural plate2.69e-0882
pre-chordal neural plate4.84e-0861
skeletal element1.23e-0790
nervous system2.04e-0789
neurectoderm4.00e-0786
ecto-epithelium8.84e-07104


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)
MA0003.112.1731
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.11.149
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.11.85223
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.11.45353
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.882847
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.671725
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00563817
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.11.15882
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.61871
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.02896
MA0103.11.76074
MA0105.10.134725
MA0106.10.70837
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.11.16614
MA0146.10.718193
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.23.52102
MA0035.20.621793
MA0039.20.35955
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.21.35181
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.10.65596
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.111.5456
MA0163.10.0270301
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.21.52352
MA0079.20.476723
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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
CTCF#1066443.573504248716680.01316635007238510.0466128961088078
E2F1#186954.089491012399440.001749817597761990.0107607136602876
E2F6#187654.180963109747820.001573598759586970.00997602773172899
EBF1#187968.9064668465692.00211291586927e-067.32394643854538e-05
EGR1#195854.156815912341780.001617966818864440.0101354868399342
ELF1#199753.548414965672950.003446837775721690.0175328409535651
EP300#203355.644951438519330.0003688138931814860.00367158080163771
GATA3#2625522.69709696433833.87517465667206e-071.88768360992618e-05
PAX5#507955.557971275981520.0003977176196612860.0038874338305854
POLR2A#543062.147453176558070.01019570676818780.0380663289301386
SPI1#668856.836936257102270.0001449641773974030.00188635855011306
TAF1#687263.343046285745290.0007162474284635620.00573651573476273
YY1#752854.092642291544880.001743365462849530.0107273520046275
ZEB1#6935514.07369334795324.14824643478507e-060.000131603496173304



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1522&oldid=2570033"