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Coexpression cluster:C3690: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;6.86157,MA0004.1;6.09481,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;9.33321,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.333427,MA0058.1;11.6775,MA0059.1;2.854,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;1.84332,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;16.7733,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;10.9535,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;1.52002,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;2.32521,MA0115.1;1.57693,MA0116.1;1.3784,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;1.12079,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;1.37817,MA0146.1;0.707589,MA0147.1;3.48176,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;4.75888,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;3.15214,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;2.97249,MA0150.1;1.76247,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;1.51687,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;4.34338,MA0163.1;4.77883,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;28.4995,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;1.40979,MA0442.1;0
}}
}}

Revision as of 21:33, 22 January 2013


Full id: C3690_CD4_CD14CD16_optic_substantia_acute_Eosinophils_migratory



Phase1 CAGE Peaks

Hg19::chr17:76124760..76124775,-p2@TMC6
Hg19::chr17:76124788..76124804,-p3@TMC6
Hg19::chr17:76124812..76124851,-p1@TMC6


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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell8.66e-52168
angioblastic mesenchymal cell8.66e-52168
hematopoietic oligopotent progenitor cell7.18e-51161
hematopoietic multipotent progenitor cell7.18e-51161
hematopoietic cell8.19e-50177
leukocyte5.82e-42136
nongranular leukocyte9.51e-37115
hematopoietic lineage restricted progenitor cell3.34e-36120
myeloid cell3.23e-33108
common myeloid progenitor3.23e-33108
myeloid leukocyte1.35e-2472
myeloid lineage restricted progenitor cell5.43e-2166
granulocyte monocyte progenitor cell4.68e-2067
monopoietic cell1.40e-1959
monocyte1.40e-1959
monoblast1.40e-1959
promonocyte1.40e-1959
defensive cell2.76e-1948
phagocyte2.76e-1948
macrophage dendritic cell progenitor5.40e-1961
classical monocyte2.34e-1642
CD14-positive, CD16-negative classical monocyte2.34e-1642
nucleate cell9.83e-1655
lymphocyte2.47e-1553
common lymphoid progenitor2.47e-1553
lymphoid lineage restricted progenitor cell3.07e-1552
mature alpha-beta T cell1.23e-1118
alpha-beta T cell1.23e-1118
immature T cell1.23e-1118
mature T cell1.23e-1118
immature alpha-beta T cell1.23e-1118
T cell3.46e-1025
pro-T cell3.46e-1025
stuff accumulating cell1.87e-0987
CD8-positive, alpha-beta T cell4.48e-0811
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.23e-2198
blood island1.23e-2198
hemolymphoid system5.99e-20108
immune system6.22e-1593
bone marrow1.51e-1476
bone element9.27e-1282
skeletal element1.51e-0990
adult organism1.73e-07114
Disease
Ontology termp-valuen
myeloid leukemia1.65e-0831
leukemia1.92e-0839
hematologic cancer7.42e-0751
immune system cancer7.42e-0751


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)
MA0003.16.86157
MA0004.16.09481
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.19.33321
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.111.6775
MA0059.12.854
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.84332
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.116.7733
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.110.9535
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.11.52002
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.12.32521
MA0115.11.57693
MA0116.11.3784
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.11.37817
MA0146.10.707589
MA0147.13.48176
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.24.75888
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.23.15214
MA0047.20.973066
MA0112.20.264678
MA0065.22.97249
MA0150.11.76247
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.14.34338
MA0163.14.77883
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.228.4995
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
ATF3#467322.46317452600878.81932387510763e-050.00129547308887815
E2F1#186934.907389214879320.008460985347239390.0325029186258261
E2F6#187635.017155731697390.00791769806886330.0321857569910483
EBF1#187938.9064668465690.00141523283560980.00914638008157502
EGR1#195834.988179094810140.008056488137383440.0320379074964851
ELF1#199734.258097958807540.01295179875054610.0461852263626155
GATA1#2623313.56030814380040.0004009615963782630.00387705102899263
HMGN3#932438.178547723350590.001827766942164210.0108620775960333
MAX#414936.452555509007120.003721913834265510.0186370503397831
SIN3A#2594235.408884726815140.006318961977991520.0276440359409985
TAF7#6879311.43306940492390.0006690181981945830.00542397078103121
TFAP2A#7020316.5186343730450.0002218033880766340.0024807157900338
TFAP2C#7022310.80922860986020.0007916746575753130.00615420242370734
USF1#739136.361499277207960.00388404057290560.019013138663871
USF2#7392312.99219738506960.0004558979393427810.00421358627318768
ZEB1#6935316.88843201754390.0002075486917327580.00242625675127351



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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