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Coexpression cluster:C1627: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;1.40197,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;1.45664,MA0017.1;1.24112,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;2.0635,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;0.195817,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.288856,MA0056.1;0,MA0057.1;1.66737,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;1.2972,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;1.43794,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;0.973423,MA0115.1;1.35895,MA0116.1;0.382106,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;0.277033,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.938075,MA0145.1;0.442008,MA0146.1;1.82062,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;3.99004,MA0062.2;2.17426,MA0035.2;0.691506,MA0039.2;0.801354,MA0138.2;0.837782,MA0002.2;1.50443,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.136971,MA0065.2;0.880827,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.98952,MA0155.1;2.57641,MA0156.1;1.20729,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.0592265,MA0163.1;0.680296,MA0164.1;0.810347,MA0080.2;1.15604,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;1.03616,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:04, 22 January 2013


Full id: C1627_Whole_Neutrophils_CD14CD16_CD14_blood_CD8_Eosinophils



Phase1 CAGE Peaks

Hg19::chr11:2323089..2323154,-p1@C11orf21
Hg19::chr11:2323349..2323407,+p1@TSPAN32
Hg19::chr12:51717875..51717920,-p1@BIN2
Hg19::chr21:46340976..46341000,+p1@ENST00000441379
p1@uc002zgh.2
Hg19::chr9:21031615..21031651,-p1@PTPLAD2


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 cell2.62e-90168
angioblastic mesenchymal cell2.62e-90168
hematopoietic oligopotent progenitor cell6.89e-85161
hematopoietic multipotent progenitor cell6.89e-85161
hematopoietic cell1.28e-82177
leukocyte2.16e-75136
hematopoietic lineage restricted progenitor cell1.35e-63120
nongranular leukocyte6.97e-61115
myeloid cell3.62e-56108
common myeloid progenitor3.62e-56108
myeloid leukocyte2.40e-4372
granulocyte monocyte progenitor cell3.71e-3867
myeloid lineage restricted progenitor cell3.33e-3766
macrophage dendritic cell progenitor1.05e-3361
monopoietic cell5.91e-3359
monocyte5.91e-3359
monoblast5.91e-3359
promonocyte5.91e-3359
defensive cell5.81e-3048
phagocyte5.81e-3048
classical monocyte5.13e-2942
CD14-positive, CD16-negative classical monocyte5.13e-2942
nucleate cell2.10e-2455
lymphocyte1.14e-2353
common lymphoid progenitor1.14e-2353
lymphoid lineage restricted progenitor cell1.82e-2352
connective tissue cell7.61e-19361
mesenchymal cell1.79e-18354
mature alpha-beta T cell3.82e-1518
alpha-beta T cell3.82e-1518
immature T cell3.82e-1518
mature T cell3.82e-1518
immature alpha-beta T cell3.82e-1518
T cell3.79e-1325
pro-T cell3.79e-1325
motile cell9.81e-13386
CD8-positive, alpha-beta T cell3.46e-1111
intermediate monocyte2.28e-099
CD14-positive, CD16-positive monocyte2.28e-099
lymphocyte of B lineage4.03e-0924
pro-B cell4.03e-0924
stuff accumulating cell8.14e-0987
multi fate stem cell1.37e-08427
stem cell2.76e-08441
granulocyte3.89e-088
somatic stem cell6.32e-08433
B cell2.12e-0714
Uber Anatomy
Ontology termp-valuen
hematopoietic system8.25e-4498
blood island8.25e-4498
hemolymphoid system6.37e-39108
bone marrow1.81e-3376
immune system4.82e-3193
bone element4.22e-2982
skeletal element1.47e-2790
skeletal system1.23e-23100
connective tissue2.02e-17371
lateral plate mesoderm5.95e-12203
blood1.23e-0815
haemolymphatic fluid1.23e-0815
organism substance1.23e-0815
adult organism2.32e-08114
musculoskeletal system2.58e-07167
Disease
Ontology termp-valuen
myeloid leukemia2.97e-1131
leukemia4.80e-1139
hematologic cancer5.26e-1051
immune system cancer5.26e-1051


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)
MA0003.11.40197
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.11.45664
MA0017.11.24112
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.12.0635
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
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.11.66737
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
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.92154
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.11.43794
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
MA0114.10.973423
MA0115.11.35895
MA0116.10.382106
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
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.938075
MA0145.10.442008
MA0146.11.82062
MA0147.10.386018
MA0148.10.653474
MA0149.13.99004
MA0062.22.17426
MA0035.20.691506
MA0039.20.801354
MA0138.20.837782
MA0002.21.50443
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.880827
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.98952
MA0155.12.57641
MA0156.11.20729
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.680296
MA0164.10.810347
MA0080.21.15604
MA0018.20.781393
MA0099.20.699641
MA0079.21.03616
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
EBF1#187935.34388010794140.01187615563868110.0432277495817175
ELF1#199754.258097958807540.0007142416939776840.0057252811633537
TAL1#6886211.94744667097610.0104757781809920.0387999077042564



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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