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Coexpression cluster:C2475: Difference between revisions

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{{Coexpression_clusters
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41,0.203996,0.276721,0.321965,0.264707,0.000388714|tfbs_overrepresentation_for_novel_motifs=1.44014,0.0888524,0.581696,0.741427,1.32255,0.739643,1.92131,1.02453,0.392841,0.902371,1.68405,0.867962,2.45508,0.809319,0.532789,0.559384,1.05593,0.471262,0.938585,0.223552,0.581762,0.975621,1.73475,0.528529,1.53003,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,1.00622,3.15145,1.75478,0.463978,2.59922,0.493145,0.66492,0.183156,1.31558,0.0946706,0.61613,1.92371,1.65941,0.173425,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,1.92893,0.393426,1.02706,1.96835,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,2.33882,0.844168,1.03184,1.27559,0.109222,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,2.92606,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,1.44917,1.14697,0.575476,0.717043,1.46636,0.489254,0.393155,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,5.50509,2.30681,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,1.73115,3.26642,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.66252,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,1.28873,0.632914,1.4628,3.18768,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.359498|tfbs_overrepresentation_jaspar=MA0003.1;0.720743,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.0695829,MA0017.1;0.577281,MA0019.1;4.80011,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.396851,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;4.16323,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.00636811,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.536981,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;2.9994,MA0117.1;2.78257,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;2.87436,MA0145.1;0.569905,MA0146.1;0.061409,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.0247757,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;0.199162,MA0150.1;1.53138,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;1.02191,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.309472,MA0163.1;0.253219,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.0626799,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2475_immature_mature_Small_serous_Bronchial_Alveolar_Tracheal
|id=C2475
}}

Latest revision as of 12:06, 17 September 2013


Full id: C2475_immature_mature_Small_serous_Bronchial_Alveolar_Tracheal



Phase1 CAGE Peaks

Hg19::chr19:11200122..11200155,+p1@LDLR
Hg19::chr19:11200163..11200180,+p2@LDLR
Hg19::chr19:11200181..11200193,+p4@LDLR
Hg19::chr19:11200194..11200207,+p5@LDLR


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
animal cell9.26e-24679
eukaryotic cell9.26e-24679
somatic cell3.13e-23588
native cell4.22e-14722
embryonic cell1.47e-13250
epithelial cell6.90e-09253
endodermal cell3.05e-0758
stuff accumulating cell9.61e-0787
Uber Anatomy
Ontology termp-valuen
trunk mesenchyme1.13e-08122
mesenchyme1.18e-08160
entire embryonic mesenchyme1.18e-08160
epithelial tube1.62e-08117
anatomical group1.68e-08625
developing anatomical structure2.40e-08581
anatomical system3.06e-08624
embryonic structure9.32e-08564
organism subdivision9.52e-08264
multi-cellular organism1.04e-07656
trunk2.36e-07199
unilaminar epithelium3.75e-07148
germ layer4.83e-07560
germ layer / neural crest4.83e-07560
embryonic tissue4.83e-07560
presumptive structure4.83e-07560
germ layer / neural crest derived structure4.83e-07560
epiblast (generic)4.83e-07560
embryo5.19e-07592


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)
MA0003.10.720743
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.14.80011
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.14.16323
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.12.9994
MA0117.12.78257
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.12.87436
MA0145.10.569905
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.11.53138
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0626799
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
BCLAF1#9774421.65264761012184.54636978835329e-060.000141652241743983
CCNT2#90546.336201576962630.0006203100587215640.00512171414521476
CEBPB#105147.971147625824820.0002476385788090830.00268095009145245
CHD2#1106410.34402283411698.73193255208051e-050.0012906231302105
E2F4#1874412.66806031528443.88145892637771e-050.000726740209415493
E2F6#187645.017155731697390.00157802193473060.00996897125824637
EGR1#195844.988179094810140.001615011500076050.0101437446509768
EP300#203346.77394172622320.0004748459821442640.00434335606316034
FOSL2#2355416.93020060456171.2165416097647e-050.000303812504022515
GTF2B#2959431.94382993432429.59435337635006e-074.08656065364039e-05
GTF2F1#2962412.73966087675773.79492332235515e-050.000718133714193604
HEY1#2346244.040111043105710.00375304636917980.018604728011713
HMGN3#932448.178547723350590.0002234570284440470.00248114273800424
IRF1#365947.63716375356390.0002938853996185490.0030748444450773
JUND#372746.994663941871030.000417684217818580.00391760413334124
MAX#414946.452555509007120.0005767613195645490.00485385781257066
MXI1#460149.96157162875930.0001015224754950450.00142339989504994
MYC#460945.22228187160940.001344309395272740.00887698083794192
PAX5#507946.669565531177830.0005052774169483260.00443786629792836
POU2F2#545249.106124057742520.000145395665174930.00188399229220899
REST#597849.650028716128020.0001152825614219170.00157016111532911
SIN3A#2594245.408884726815140.001168172384885160.00796310656647874
SP1#666745.69838137814090.0009482606065333980.00684135047566604
SREBF1#6720447.00584944048832.04523668136926e-071.10217994719053e-05
SREBF2#67214436.9432624113482.70480926640298e-113.17401769633552e-09
STAT1#6772420.70658749719925.43610708103893e-060.000165281393722453
STAT2#6773465.26377118644075.50053512607993e-083.46483949356249e-06
STAT3#6774410.51946499715428.16377768286615e-050.00123139338160147
TAF1#687243.343046285745290.008005664898701650.0322222767209612
TAF7#6879411.43306940492395.85061525419808e-050.000968969880325394
TAL1#6886429.86861667744021.25525650806991e-065.04028198563295e-05
TBP#690843.706770687096390.005296377814784350.0244215630286209
TCF12#6938410.63446490218647.8163066689251e-050.00120048125322922
YY1#752844.911170749853860.00171871838055440.0106865052656261



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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