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Coexpression cluster:C615: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.554539,1.11028,0.541316,0.297884,0.467499,0.296522,0.360887,0.0785261,0.562966,0.0330948,0.271739,0.398649,0.446874,0.925865,0.152923,0.169541,0.560096,0.117033,0.480243,0.20952,0.184,0.440546,0.789382,0.150321,0.623871,0.418678,0.392469,0.288329,0.920659,0.352289,0.254115,0.594213,0.658757,0.205943,1.31633,1.33942,0.801546,0.29748,0.113038,0.881025,0.129369,0.241157,0.142503,0.151865,0.664236,0.596593,0.361827,0.262957,0.00898478,0.15614,0.431291,0.372023,0.259277,0.666176,0.811691,0.353512,0.15913,0.325599,0.987553,0.324748,0.632472,0.363871,0.0774141,0.534578,0.379438,0.503101,0.896916,1.25738,0.584559,1.09778,0.652781,0.278952,2.50231,0.80977,0.196336,1.0948,0.16121,0.519091,0.581542,0.213774,0.0636623,0.533593,0.37913,0.274429,0.760489,3.41665,0.656421,0.340238,0.454557,1.35556,0.98765,0.734737,0.609873,0.101133,0.913764,0.109261,0.823754,0.649779,0.458696,0.12702,0.365546,0.6046,0.644537,0.563483,0.492631,0.268065,1.35334,0.348037,0.623411,0.439869,0.561401,0.641937,0.179896,0.765049,0.940917,0.12714,0.923071,0.253155,0.500972,0.102878,0.801818,0.452379,0.294241,0.388967,1.04884,0.519787,0.355419,0.614537,0.842806,0.354951,0.735394,0.256408,0.856671,0.386057,1.00021,0.138272,0.249339,0.288795,0.95886,1.80749,1.40745,0.922589,0.356906,0.646464,2.14184,2.34127,0.47912,1.64894,0.238532,0.66991,0.230014,3.18004,0.735758,0.921167,0.363452,1.12781,0.440071,0.144217,0.218554,0.571801,0.921409,0.718143,0.580811,0.577588,0.508869,0.378443,0.0919059,0.35974,3.68302
|tfbs_overrepresentation_jaspar=MA0003.1;3.54937,MA0004.1;0.757232,MA0006.1;0.464315,MA0007.1;0.260673,MA0009.1;0.695988,MA0014.1;4.13871,MA0017.1;0.181071,MA0019.1;0.403106,MA0024.1;0.59663,MA0025.1;0.824398,MA0027.1;2.28954,MA0028.1;0.492785,MA0029.1;0.614815,MA0030.1;0.604021,MA0031.1;0.543644,MA0038.1;0.363295,MA0040.1;0.620334,MA0041.1;0.291389,MA0042.1;0.73203,MA0043.1;0.69629,MA0046.1;0.685589,MA0048.1;0.110534,MA0050.1;0.265714,MA0051.1;0.359609,MA0052.1;0.623986,MA0055.1;0.45122,MA0056.1;0,MA0057.1;1.12385,MA0058.1;0.580064,MA0059.1;0.57771,MA0060.1;0.564002,MA0061.1;0.487876,MA0063.1;0,MA0066.1;0.363668,MA0067.1;1.00375,MA0068.1;0.169955,MA0069.1;0.681911,MA0070.1;0.671241,MA0071.1;0.329767,MA0072.1;0.666958,MA0073.1;4.87356,MA0074.1;0.358953,MA0076.1;0.609177,MA0077.1;0.65962,MA0078.1;0.447828,MA0081.1;0.199203,MA0083.1;0.703169,MA0084.1;1.18798,MA0087.1;0.664629,MA0088.1;2.27574,MA0089.1;0,MA0090.1;0.223576,MA0091.1;0.278153,MA0092.1;0.247341,MA0093.1;0.469677,MA0095.1;0,MA0098.1;0,MA0100.1;0.375452,MA0101.1;0.1571,MA0103.1;0.448026,MA0105.1;1.85962,MA0106.1;0.399649,MA0107.1;0.107387,MA0108.2;0.540797,MA0109.1;0,MA0111.1;0.234271,MA0113.1;0.414278,MA0114.1;0.104181,MA0115.1;0.929032,MA0116.1;2.35038,MA0117.1;0.732,MA0119.1;1.65283,MA0122.1;0.756889,MA0124.1;0.888592,MA0125.1;0.807083,MA0130.1;0,MA0131.1;0.464307,MA0132.1;0,MA0133.1;0,MA0135.1;0.725055,MA0136.1;0.369468,MA0139.1;0.789887,MA0140.1;0.873545,MA0141.1;0.574537,MA0142.1;0.514195,MA0143.1;0.414436,MA0144.1;0.652118,MA0145.1;0.827687,MA0146.1;1.84907,MA0147.1;1.19725,MA0148.1;0.296708,MA0149.1;0.319221,MA0062.2;0.819072,MA0035.2;0.872194,MA0039.2;4.66501,MA0138.2;0.44894,MA0002.2;0.0708857,MA0137.2;0.504333,MA0104.2;1.42323,MA0047.2;0.388882,MA0112.2;0.515321,MA0065.2;0.16797,MA0150.1;0.218956,MA0151.1;0,MA0152.1;0.333125,MA0153.1;0.790794,MA0154.1;1.83273,MA0155.1;0.138832,MA0156.1;0.170442,MA0157.1;0.489002,MA0158.1;0,MA0159.1;0.112236,MA0160.1;0.30953,MA0161.1;0,MA0162.1;4.46014,MA0163.1;3.32868,MA0164.1;0.425415,MA0080.2;0.46983,MA0018.2;1.82761,MA0099.2;0.333432,MA0079.2;11.1663,MA0102.2;1.22472,MA0258.1;0.089643,MA0259.1;0.753086,MA0442.1;0
}}
}}

Revision as of 19:19, 22 January 2013


Full id: C615_CD19_Neutrophils_Eosinophils_CD4_CD8_Natural_blood



Phase1 CAGE Peaks

Hg19::chr10:69644837..69644886,-p@chr10:69644837..69644886
-
Hg19::chr11:65407297..65407328,+p6@SIPA1
Hg19::chr16:30662050..30662078,+p5@PRR14
Hg19::chr19:4067174..4067200,-p9@ZBTB7A
Hg19::chr19:49842573..49842602,+p@chr19:49842573..49842602
+
Hg19::chr19:49843537..49843640,+p@chr19:49843537..49843640
+
Hg19::chr19:58694742..58694800,+p2@ZNF274
Hg19::chr20:18774702..18774738,+p1@LOC100270804
Hg19::chr20:5591566..5591598,-p2@GPCPD1
Hg19::chr22:38073174..38073215,-p@chr22:38073174..38073215
-
Hg19::chr2:197890756..197890770,-p@chr2:197890756..197890770
-
Hg19::chr2:198175495..198175525,-p1@ANKRD44
Hg19::chr4:78740511..78740539,-p1@CNOT6L
Hg19::chr8:101322317..101322334,-p2@RNF19A


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:0005515protein binding0.0233065486029287
GO:0046582Rap GTPase activator activity0.0233065486029287
GO:0016564transcription repressor activity0.0233065486029287
GO:0035035histone acetyltransferase binding0.026484607892999



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
leukocyte3.62e-59136
hematopoietic stem cell3.45e-58168
angioblastic mesenchymal cell3.45e-58168
hematopoietic cell1.31e-54177
hematopoietic oligopotent progenitor cell3.95e-54161
hematopoietic multipotent progenitor cell3.95e-54161
hematopoietic lineage restricted progenitor cell7.15e-48120
nongranular leukocyte9.84e-48115
myeloid cell1.39e-28108
common myeloid progenitor1.39e-28108
myeloid leukocyte1.60e-2872
granulocyte monocyte progenitor cell1.47e-2467
lymphocyte1.94e-2353
common lymphoid progenitor1.94e-2353
lymphoid lineage restricted progenitor cell3.31e-2352
myeloid lineage restricted progenitor cell8.78e-2366
nucleate cell1.48e-2255
macrophage dendritic cell progenitor4.03e-2261
monopoietic cell2.16e-2159
monocyte2.16e-2159
monoblast2.16e-2159
promonocyte2.16e-2159
defensive cell7.09e-2148
phagocyte7.09e-2148
classical monocyte4.02e-2042
CD14-positive, CD16-negative classical monocyte4.02e-2042
mature alpha-beta T cell4.37e-1218
alpha-beta T cell4.37e-1218
immature T cell4.37e-1218
mature T cell4.37e-1218
immature alpha-beta T cell4.37e-1218
T cell9.96e-1225
pro-T cell9.96e-1225
lymphocyte of B lineage7.69e-1124
pro-B cell7.69e-1124
B cell8.53e-0914
CD8-positive, alpha-beta T cell4.71e-0811
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.85e-3198
blood island2.85e-3198
hemolymphoid system2.32e-29108
immune system5.36e-2293
bone marrow1.05e-2076
adult organism3.71e-20114
bone element1.91e-1882
skeletal element7.15e-1490
skeletal system2.70e-11100
blood8.28e-0915
haemolymphatic fluid8.28e-0915
organism substance8.28e-0915
neural tube8.62e-0856
neural rod8.62e-0856
future spinal cord8.62e-0856
neural keel8.62e-0856
regional part of nervous system3.31e-0753
regional part of brain3.31e-0753


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)
MA0003.13.54937
MA0004.10.757232
MA0006.10.464315
MA0007.10.260673
MA0009.10.695988
MA0014.14.13871
MA0017.10.181071
MA0019.10.403106
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.10.492785
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.10.363295
MA0040.10.620334
MA0041.10.291389
MA0042.10.73203
MA0043.10.69629
MA0046.10.685589
MA0048.10.110534
MA0050.10.265714
MA0051.10.359609
MA0052.10.623986
MA0055.10.45122
MA0056.10
MA0057.11.12385
MA0058.10.580064
MA0059.10.57771
MA0060.10.564002
MA0061.10.487876
MA0063.10
MA0066.10.363668
MA0067.11.00375
MA0068.10.169955
MA0069.10.681911
MA0070.10.671241
MA0071.10.329767
MA0072.10.666958
MA0073.14.87356
MA0074.10.358953
MA0076.10.609177
MA0077.10.65962
MA0078.10.447828
MA0081.10.199203
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.12.27574
MA0089.10
MA0090.10.223576
MA0091.10.278153
MA0092.10.247341
MA0093.10.469677
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.10.1571
MA0103.10.448026
MA0105.11.85962
MA0106.10.399649
MA0107.10.107387
MA0108.20.540797
MA0109.10
MA0111.10.234271
MA0113.10.414278
MA0114.10.104181
MA0115.10.929032
MA0116.12.35038
MA0117.10.732
MA0119.11.65283
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.369468
MA0139.10.789887
MA0140.10.873545
MA0141.10.574537
MA0142.10.514195
MA0143.10.414436
MA0144.10.652118
MA0145.10.827687
MA0146.11.84907
MA0147.11.19725
MA0148.10.296708
MA0149.10.319221
MA0062.20.819072
MA0035.20.872194
MA0039.24.66501
MA0138.20.44894
MA0002.20.0708857
MA0137.20.504333
MA0104.21.42323
MA0047.20.388882
MA0112.20.515321
MA0065.20.16797
MA0150.10.218956
MA0151.10
MA0152.10.333125
MA0153.10.790794
MA0154.11.83273
MA0155.10.138832
MA0156.10.170442
MA0157.10.489002
MA0158.10
MA0159.10.112236
MA0160.10.30953
MA0161.10
MA0162.14.46014
MA0163.13.32868
MA0164.10.425415
MA0080.20.46983
MA0018.21.82761
MA0099.20.333432
MA0079.211.1663
MA0102.21.22472
MA0258.10.089643
MA0259.10.753086
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
E2F6#187682.866946132398510.002341652686038430.0132739831131767
EGR1#195872.494089547405070.01176051944619070.0428576325217458
ELF1#1997103.041498542005380.0001960883233653430.00235800442187139
ETS1#211353.474557472215120.01035429153034180.0384481210672461
GABPB1#255363.029007358363790.008662589686335660.0329717629742779
HEY1#2346282.308634881774690.009675141623558980.0364091131057139
HMGN3#932463.505091881435970.004171546858416660.0198701168633667
JUND#372762.997713117944730.009116463920820550.034495647818071
PAX5#507962.858385227647640.01150092546436290.0420672137629178
POLR2A#5430131.994063663946780.0003845688903765380.00377445638023073
POU2F2#545253.252187163479470.01362351556019460.0480717055744024
TAF1#6872112.626679224514160.0002393683783156760.00260573213080163
TBP#690892.382924013133390.003811761126235160.0188252007501241
YY1#752882.806383285630770.002702639654839410.0148667956869152
ZBTB7A#5134184.201091033071940.0001628644135476470.00202661700065562



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:C615&oldid=2569126"