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Coexpression cluster:C1558: Difference between revisions

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{{Coexpression_clusters
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384437,1.55551,0.44943,1.35492,0.802434,0.25115,0.642741,1.16016,0.659743,0.598009,1.00172,0.359091,0.27659,0.417272,0.195238,1.06371,0.654459,0.388123,0.815792,0.415749,0.580638,0.132849,0.451846,0.824538,1.32072,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,1.64682,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,1.05625,1.23387,1.36104,0.709554,0.675933,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.536557,0.49825,0.228496,1.96782,1.79645,1.41984,1.15413,1.01895,0.367039,1.15465,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,2.40164,0.967698,0.88799,1.49565,2.18702,0.717647,0.549347,1.11542,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.597842,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.995523,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.526389,1.29319,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.923751,0.731946,1.89906|tfbs_overrepresentation_jaspar=MA0003.1;0.737422,MA0004.1;0.626788,MA0006.1;1.14863,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;3.07977,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;0.470679,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;1.08193,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.603517,MA0056.1;0,MA0057.1;0.189508,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;0.291022,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.551452,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;1.92154,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;0.442769,MA0105.1;0.520776,MA0106.1;0.779931,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,MA0113.1;0.797251,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;0.382106,MA0117.1;2.59297,MA0119.1;0.504689,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;3.29691,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;0.277033,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.442008,MA0146.1;0.946108,MA0147.1;1.00307,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.777733,MA0035.2;0.691506,MA0039.2;2.38271,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;1.54865,MA0047.2;0.767096,MA0112.2;1.35805,MA0065.2;0.146576,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;1.3196,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;1.23503,MA0163.1;1.49262,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;2.79313,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;1.02361,MA0442.1;0}}
|full_id=C1558_CD19_CD8_CD4_Mesenchymal_MCF7_CD14CD16_CD14
|id=C1558
}}

Latest revision as of 11:47, 17 September 2013


Full id: C1558_CD19_CD8_CD4_Mesenchymal_MCF7_CD14CD16_CD14



Phase1 CAGE Peaks

Hg19::chr10:104614236..104614277,-p@chr10:104614236..104614277
-
Hg19::chr16:2827358..2827403,+p1@AK056451
Hg19::chr1:245027971..245027998,+p@chr1:245027971..245027998
+
Hg19::chr5:43484033..43484098,+p1@ENST00000504469
Hg19::chr8:135725363..135725407,+p@chr8:135725363..135725407
+


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
leukocyte1.37e-38136
hematopoietic stem cell3.19e-34168
angioblastic mesenchymal cell3.19e-34168
hematopoietic cell5.88e-34177
hematopoietic lineage restricted progenitor cell2.49e-32120
hematopoietic oligopotent progenitor cell3.97e-31161
hematopoietic multipotent progenitor cell3.97e-31161
nongranular leukocyte4.11e-30115
myeloid leukocyte2.47e-1872
nucleate cell2.90e-1655
classical monocyte3.28e-1642
CD14-positive, CD16-negative classical monocyte3.28e-1642
lymphoid lineage restricted progenitor cell7.40e-1652
lymphocyte1.13e-1553
common lymphoid progenitor1.13e-1553
myeloid lineage restricted progenitor cell1.44e-1566
myeloid cell1.86e-15108
common myeloid progenitor1.86e-15108
granulocyte monocyte progenitor cell3.24e-1567
defensive cell2.29e-1448
phagocyte2.29e-1448
macrophage dendritic cell progenitor4.36e-1461
monopoietic cell2.17e-1359
monocyte2.17e-1359
monoblast2.17e-1359
promonocyte2.17e-1359
mature alpha-beta T cell3.76e-1118
alpha-beta T cell3.76e-1118
immature T cell3.76e-1118
mature T cell3.76e-1118
immature alpha-beta T cell3.76e-1118
T cell2.97e-0825
pro-T cell2.97e-0825
CD8-positive, alpha-beta T cell3.24e-0811
B cell1.28e-0714
lymphocyte of B lineage2.32e-0724
pro-B cell2.32e-0724
mesenchymal cell4.19e-07354
motile cell6.69e-07386
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.36e-2098
blood island1.36e-2098
hemolymphoid system1.28e-18108
bone marrow2.79e-1576
immune system2.18e-1493
bone element1.74e-1282
skeletal element2.95e-0990
regional part of nervous system1.63e-0853
regional part of brain1.63e-0853
neural tube3.14e-0856
neural rod3.14e-0856
future spinal cord3.14e-0856
neural keel3.14e-0856
lateral plate mesoderm3.78e-08203
skeletal system2.63e-07100


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)
MA0003.10.737422
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.13.07977
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
MA0048.11.08193
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.603517
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.551452
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.92154
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
MA0105.10.520776
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
MA0117.12.59297
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.13.29691
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.10.946108
MA0147.11.00307
MA0148.10.653474
MA0149.10.681935
MA0062.20.777733
MA0035.20.691506
MA0039.22.38271
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.21.54865
MA0047.20.767096
MA0112.21.35805
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.11.3196
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.11.23503
MA0163.11.49262
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.22.79313
MA0102.21.66336
MA0258.10.345771
MA0259.11.02361
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#90545.068961261570110.002709998091280770.0148876698046011
E2F6#187644.013724585357910.006632118233933880.0282830459874978
ELF1#199743.406478367046030.01235066105299550.0447179992967167
ETS1#211347.783008737761870.0005121035947688870.00443847197793094
GTF2B#2959425.55506394745944.67711684449311e-060.000145206125482169
GTF2F1#296237.643796526054590.00428415496412050.0203424805773031
HEY1#2346254.040111043105710.0009288852205177990.00673412769302085
IRF1#365946.109731002851120.001315525264767990.00880493098738173
MYC#460955.22228187160940.0002573944848850610.00276194622489581
NFKB1#479044.390450739355070.004707732692524960.022192322034512
NRF1#489937.326167668626540.004839689817117540.0226833175429672
REST#597835.790017229676810.009468788694433940.0356827171270111
SIX5#147912310.25202921327540.001832291068677690.0108469927968274
TAF1#687253.343046285745290.002394600090870310.0135081364853843
TAF7#687936.859841642954350.005843286407019040.0262378859393208
TBP#690853.706770687096390.001428755106721120.00917529081908918
TCF12#693836.380678941311850.007185168653258840.0298232187019196
YY1#752854.911170749853860.00034993140821360.00352357176459893
ZNF143#770238.100525931336740.003624870512090980.0183259682162973



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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