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Coexpression cluster:C3606: Difference between revisions

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{{Coexpression_clusters
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transmembrane transporter activity!0.0041209802018991!5306$GO:0008526!phosphatidylinositol transporter activity!0.00618110637118426!5306$GO:0005548!phospholipid transporter activity!0.0219688562324111!5306$GO:0005319!lipid transporter activity!0.049383343269881!5306|id=C3606|ontology_enrichment_celltype=CL:0000766!1.59e-23!72;CL:0000557!2.47e-20!67;CL:0000473!3.75e-20!48;CL:0000234!3.75e-20!48;CL:0002009!4.71e-19!61;CL:0000839!2.58e-18!66;CL:0002194!5.77e-18!59;CL:0000576!5.77e-18!59;CL:0000040!5.77e-18!59;CL:0000559!5.77e-18!59;CL:0000860!6.60e-18!42;CL:0002057!6.60e-18!42;CL:0000325!2.40e-13!87;CL:0000763!6.96e-13!108;CL:0000049!6.96e-13!108;CL:0000115!1.39e-08!36;CL:0000738!2.59e-07!136|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0007023!6.61e-25!114;UBERON:0001049!8.21e-20!56;UBERON:0005068!8.21e-20!56;UBERON:0006241!8.21e-20!56;UBERON:0007135!8.21e-20!56;UBERON:0000073!1.40e-18!53;UBERON:0002616!1.40e-18!53;UBERON:0003075!4.12e-17!82;UBERON:0007284!4.12e-17!82;UBERON:0002193!3.39e-16!108;UBERON:0002405!8.29e-16!93;UBERON:0002371!6.64e-15!76;UBERON:0002346!1.24e-14!86;UBERON:0002390!1.59e-14!98;UBERON:0003061!1.59e-14!98;UBERON:0001017!2.27e-14!81;UBERON:0000955!3.35e-14!68;UBERON:0006238!3.35e-14!68;UBERON:0002780!3.53e-14!41;UBERON:0001890!3.53e-14!41;UBERON:0003080!3.53e-14!41;UBERON:0006240!3.53e-14!41;UBERON:0001016!4.19e-14!89;UBERON:0001474!8.76e-14!82;UBERON:0001893!1.59e-13!34;UBERON:0003528!2.09e-13!34;UBERON:0002020!2.09e-13!34;UBERON:0001869!1.05e-12!32;UBERON:0002791!1.94e-12!32;UBERON:0010371!6.21e-12!104;UBERON:0000480!1.05e-11!625;UBERON:0003081!1.16e-11!203;UBERON:0000467!1.47e-11!624;UBERON:0003056!1.67e-11!61;UBERON:0002619!2.79e-11!22;UBERON:0004765!5.81e-11!90;UBERON:0001950!1.90e-10!20;UBERON:0000062!1.96e-10!503;UBERON:0000923!3.11e-10!560;UBERON:0010316!3.11e-10!560;UBERON:0005291!3.11e-10!560;UBERON:0006598!3.11e-10!560;UBERON:0010317!3.11e-10!560;UBERON:0002532!3.11e-10!560;UBERON:0002050!6.53e-10!564;UBERON:0000922!7.20e-10!592;UBERON:0010314!8.39e-10!132;UBERON:0001434!8.77e-10!100;UBERON:0005423!9.73e-10!581;UBERON:0000956!1.23e-09!25;UBERON:0000203!1.23e-09!25;UBERON:0004111!1.58e-09!240;UBERON:0000468!4.29e-09!656;UBERON:0004121!5.09e-09!171;UBERON:0000924!5.09e-09!171;UBERON:0006601!5.09e-09!171;UBERON:0000025!4.44e-08!192;UBERON:0000477!3.45e-07!373;UBERON:0003076!6.16e-07!15;UBERON:0003057!6.16e-07!15|pathway_enrichment=3.91018877356111e-05;0.0247514949366418;2;179;EGFR1 Signaling Pathway 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0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.0229018,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.0232618,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,2.0185,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,1.11965,0.599922,0.137917,2.47502,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.901413,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,1.5923,1.45054,1.92922,1.06461,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,6.48145,0.303648,0.993996,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,2.40384,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,2.55998,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,1.66424,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,1.33389,2.3415,5.59159,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,6.28676|tfbs_overrepresentation_jaspar=MA0003.1;6.86157,MA0004.1;0.826076,MA0006.1;2.61424,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;2.44638,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;1.62115,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;1.59304,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.407479,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;2.03569,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;1.5295,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;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,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;1.6959,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.752137,MA0146.1;7.1063,MA0147.1;3.48176,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;7.95144,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;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,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;1.2663,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;8.812,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;1.40979,MA0442.1;0}}
|full_id=C3606_CD14_Eosinophils_retina_Neutrophils_locus_pons_occipital
|gostat_on_coexpression_clusters=GO:0008525!phosphatidylcholine transmembrane transporter activity!0.0041209802018991!5306$GO:0008526!phosphatidylinositol transporter activity!0.00618110637118426!5306$GO:0005548!phospholipid transporter activity!0.0219688562324111!5306$GO:0005319!lipid transporter activity!0.049383343269881!5306
|id=C3606
}}

Latest revision as of 12:29, 17 September 2013


Full id: C3606_CD14_Eosinophils_retina_Neutrophils_locus_pons_occipital



Phase1 CAGE Peaks

Hg19::chr17:1466030..1466129,-p1@PITPNA
Hg19::chr9:135996537..135996544,-p9@RALGDS
Hg19::chr9:135996616..135996640,-p1@RALGDS


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

p.valueFDRnGenesnPathwayName
3.91018877356111e-050.02475149493664182179EGFR1 Signaling Pathway (Wikipathways):WP437



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

GO IDGO nameFDR corrected p-value
GO:0008525phosphatidylcholine transmembrane transporter activity0.0041209802018991
GO:0008526phosphatidylinositol transporter activity0.00618110637118426
GO:0005548phospholipid transporter activity0.0219688562324111
GO:0005319lipid transporter activity0.049383343269881



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>

Uber Anatomy
Ontology termp-valuen
adult organism6.61e-25114
neural tube8.21e-2056
neural rod8.21e-2056
future spinal cord8.21e-2056
neural keel8.21e-2056
regional part of nervous system1.40e-1853
regional part of brain1.40e-1853
neural plate4.12e-1782
presumptive neural plate4.12e-1782
hemolymphoid system3.39e-16108
immune system8.29e-1693
bone marrow6.64e-1576
neurectoderm1.24e-1486
hematopoietic system1.59e-1498
blood island1.59e-1498
central nervous system2.27e-1481
brain3.35e-1468
future brain3.35e-1468
regional part of forebrain3.53e-1441
forebrain3.53e-1441
anterior neural tube3.53e-1441
future forebrain3.53e-1441
nervous system4.19e-1489
bone element8.76e-1482
telencephalon1.59e-1334
brain grey matter2.09e-1334
gray matter2.09e-1334
cerebral hemisphere1.05e-1232
regional part of telencephalon1.94e-1232
ecto-epithelium6.21e-12104
anatomical group1.05e-11625
lateral plate mesoderm1.16e-11203
anatomical system1.47e-11624
pre-chordal neural plate1.67e-1161
regional part of cerebral cortex2.79e-1122
skeletal element5.81e-1190
neocortex1.90e-1020
organ1.96e-10503
germ layer3.11e-10560
germ layer / neural crest3.11e-10560
embryonic tissue3.11e-10560
presumptive structure3.11e-10560
germ layer / neural crest derived structure3.11e-10560
epiblast (generic)3.11e-10560
embryonic structure6.53e-10564
embryo7.20e-10592
structure with developmental contribution from neural crest8.39e-10132
skeletal system8.77e-10100
developing anatomical structure9.73e-10581
cerebral cortex1.23e-0925
pallium1.23e-0925
anatomical conduit1.58e-09240
multi-cellular organism4.29e-09656
ectoderm-derived structure5.09e-09171
ectoderm5.09e-09171
presumptive ectoderm5.09e-09171
tube4.44e-08192
anatomical cluster3.45e-07373
posterior neural tube6.16e-0715
chordal neural plate6.16e-0715


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
MA0004.10.826076
MA0006.12.61424
MA0007.10.804807
MA0009.11.3275
MA0014.12.44638
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
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.407479
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.12.03569
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.11.5295
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
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
MA0141.11.6959
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.17.1063
MA0147.13.48176
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.27.95144
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.23.15214
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.14.34338
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.28.812
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
CCNT2#90536.336201576962630.003930750035764890.0189793621352404
E2F6#187635.017155731697390.00791769806886330.0321607213991138
EGR1#195834.988179094810140.008056488137383440.0320123103249197
ELF1#199734.258097958807540.01295179875054610.0461568589950277
IRF1#365937.63716375356390.002244692747297240.0127903031171901
SIN3A#2594235.408884726815140.006318961977991520.0276255209518798
SMC3#9126210.02995522995520.0126656379767470.0457347634980286
USF1#739136.361499277207960.00388404057290560.0190033408317103



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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