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Coexpression cluster:C1989: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.26722,0.452433,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.859849,0.106358,0.621241,0.778743,0.274093,0.721271,0.453496,2.09103,0.963929,0.395009,1.42981,0.501863,0.500405,0.384437,0.645033,1.14094,0.549618,0.802434,0.700122,1.55072,0.458349,0.659743,0.598009,1.00172,0.94379,0.27659,2.81341,1.1597,3.81581,0.654459,1.00769,0.301779,0.415749,0.580638,0.132849,0.451846,0.476793,1.32072,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.86107,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.554326,1.23387,1.36104,0.255232,0.240727,0.917983,0.987729,0.543014,1.44891,0.934302,0.755403,0.327263,1.18161,1.37242,0.49825,0.228496,0.844289,1.79645,1.41984,2.59889,1.01895,0.367039,0.455791,0.381528,0.28626,3.93669,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,3.7711,1.37132,1.05995,0.285668,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.79475,1.15522,0.840171,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,2.92355
|tfbs_overrepresentation_jaspar=MA0003.1;3.23705,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.161847,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;0.288856,MA0056.1;0,MA0057.1;0.554727,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;0.362215,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;1.3271,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;0.994489,MA0117.1;1.1512,MA0119.1;1.25946,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;0.855546,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;2.96863,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.143698,MA0146.1;1.82062,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.777733,MA0035.2;0.691506,MA0039.2;0.0118463,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;1.96224,MA0065.2;0.146576,MA0150.1;0.550239,MA0151.1;0,MA0152.1;1.66846,MA0153.1;1.21379,MA0154.1;4.65737,MA0155.1;0.813062,MA0156.1;1.20729,MA0157.1;0.883854,MA0158.1;0,MA0159.1;1.00463,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.469165,MA0163.1;1.99104,MA0164.1;0.810347,MA0080.2;1.15604,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;2.12087,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:20, 22 January 2013


Full id: C1989_CD14_Hepatocyte_Peripheral_Basophils_Mast_dura_liver



Phase1 CAGE Peaks

Hg19::chr7:151554211..151554214,-p@chr7:151554211..151554214
-
Hg19::chr7:151574171..151574187,-p19@PRKAG2
Hg19::chr7:151574191..151574215,-p4@PRKAG2
Hg19::chr7:151574231..151574246,-p12@PRKAG2
Hg19::chr7:151574445..151574459,-p10@PRKAG2


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
leukocyte7.39e-46136
nongranular leukocyte1.36e-42115
hematopoietic lineage restricted progenitor cell1.05e-41120
macrophage dendritic cell progenitor1.15e-4161
granulocyte monocyte progenitor cell3.25e-4167
monopoietic cell1.55e-4059
monocyte1.55e-4059
monoblast1.55e-4059
promonocyte1.55e-4059
defensive cell2.29e-3948
phagocyte2.29e-3948
myeloid lineage restricted progenitor cell4.87e-3966
myeloid leukocyte8.71e-3972
classical monocyte8.01e-3642
CD14-positive, CD16-negative classical monocyte8.01e-3642
hematopoietic stem cell1.69e-35168
angioblastic mesenchymal cell1.69e-35168
hematopoietic cell3.20e-34177
hematopoietic oligopotent progenitor cell9.10e-33161
hematopoietic multipotent progenitor cell9.10e-33161
myeloid cell3.81e-27108
common myeloid progenitor3.81e-27108
stuff accumulating cell4.07e-1887
mature alpha-beta T cell5.85e-1018
alpha-beta T cell5.85e-1018
immature T cell5.85e-1018
mature T cell5.85e-1018
immature alpha-beta T cell5.85e-1018
intermediate monocyte1.98e-089
CD14-positive, CD16-positive monocyte1.98e-089
T cell2.05e-0825
pro-T cell2.05e-0825
CD8-positive, alpha-beta T cell1.52e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.18e-4298
blood island2.18e-4298
hemolymphoid system2.00e-37108
bone marrow5.67e-3476
bone element6.96e-3282
immune system1.72e-2993
adult organism2.31e-28114
skeletal element1.40e-2690
skeletal system5.76e-23100
lateral plate mesoderm8.55e-10203
blood8.36e-0915
haemolymphatic fluid8.36e-0915
organism substance8.36e-0915
regional part of cerebral cortex6.20e-0722


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)
MA0003.13.23705
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.161847
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
MA0055.10.288856
MA0056.10
MA0057.10.554727
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
MA0073.10.362215
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.3271
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
MA0116.10.994489
MA0117.11.1512
MA0119.11.25946
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
MA0145.10.143698
MA0146.11.82062
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.777733
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.21.96224
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.11.66846
MA0153.11.21379
MA0154.14.65737
MA0155.10.813062
MA0156.11.20729
MA0157.10.883854
MA0158.10
MA0159.11.00463
MA0160.10.669748
MA0161.10
MA0162.10.469165
MA0163.11.99104
MA0164.10.810347
MA0080.21.15604
MA0018.20.781393
MA0099.20.699641
MA0079.22.12087
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
CTCF#1066444.288205098460020.005152015588243280.0239451451212914
E2F1#186943.925911371903460.007214984547106360.0298840282020718
E2F6#187644.013724585357910.006632118233933880.0283050057714773
ELF1#199743.406478367046030.01235066105299550.0447428176389675
ESR1#2099424.61488263692365.42856809638808e-060.000165630798544749
MYC#460944.177825497287520.005691969036823440.0256920889548277
SMARCB1#6598414.60217262492594.30486693344344e-050.000768803005577803



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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