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Coexpression cluster:C616: Difference between revisions

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{{Coexpression_clusters
{
|full_id=C616_CD14_Natural_CD8_Basophils_Mast_Eosinophils_CD4

Latest revision as of 11:27, 17 September 2013


Full id: C616_CD14_Natural_CD8_Basophils_Mast_Eosinophils_CD4



Phase1 CAGE Peaks

Hg19::chr10:70716856..70716871,-p@chr10:70716856..70716871
-
Hg19::chr11:65189036..65189061,+p@chr11:65189036..65189061
+
Hg19::chr12:3982744..3982748,+p@chr12:3982744..3982748
+
Hg19::chr12:9917411..9917425,-p@chr12:9917411..9917425
-
Hg19::chr13:41557163..41557168,+p@chr13:41557163..41557168
+
Hg19::chr17:40540898..40540910,+p@chr17:40540898..40540910
+
Hg19::chr19:14485996..14486000,-p@chr19:14485996..14486000
-
Hg19::chr20:1305835..1305872,-p@chr20:1305835..1305872
-
Hg19::chr2:145275236..145275249,+p@chr2:145275236..145275249
+
Hg19::chr4:103790462..103790537,+p4@CISD2
Hg19::chr5:43018230..43018260,+p1@ENST00000509036
Hg19::chr7:644391..644410,+p@chr7:644391..644410
+
Hg19::chr8:29940840..29940888,+p@chr8:29940840..29940888
+
Hg19::chr9:132890689..132890715,+p@chr9:132890689..132890715
+


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
leukocyte1.01e-85136
hematopoietic stem cell4.96e-75168
angioblastic mesenchymal cell4.96e-75168
hematopoietic cell6.98e-74177
hematopoietic lineage restricted progenitor cell2.71e-71120
hematopoietic oligopotent progenitor cell8.71e-71161
hematopoietic multipotent progenitor cell8.71e-71161
nongranular leukocyte7.65e-68115
classical monocyte3.47e-5242
CD14-positive, CD16-negative classical monocyte3.47e-5242
myeloid leukocyte2.32e-4972
defensive cell1.31e-4348
phagocyte1.31e-4348
granulocyte monocyte progenitor cell7.52e-4367
myeloid cell6.43e-41108
common myeloid progenitor6.43e-41108
myeloid lineage restricted progenitor cell2.74e-4066
macrophage dendritic cell progenitor3.14e-3861
monopoietic cell1.38e-3659
monocyte1.38e-3659
monoblast1.38e-3659
promonocyte1.38e-3659
lymphoid lineage restricted progenitor cell1.26e-2652
lymphocyte7.08e-2653
common lymphoid progenitor7.08e-2653
nucleate cell1.85e-2455
mesenchymal cell3.29e-20354
connective tissue cell3.49e-19361
stuff accumulating cell3.79e-1987
mature alpha-beta T cell1.79e-1618
alpha-beta T cell1.79e-1618
immature T cell1.79e-1618
mature T cell1.79e-1618
immature alpha-beta T cell1.79e-1618
motile cell1.30e-15386
T cell3.89e-1325
pro-T cell3.89e-1325
stem cell4.75e-12441
multi fate stem cell8.21e-12427
intermediate monocyte1.65e-119
CD14-positive, CD16-positive monocyte1.65e-119
somatic stem cell3.12e-11433
lymphocyte of B lineage3.79e-1124
pro-B cell3.79e-1124
CD8-positive, alpha-beta T cell7.49e-0911
CD4-positive, alpha-beta T cell7.71e-096
granulocyte2.40e-088
B cell3.13e-0714
blood cell3.18e-0711
histamine secreting cell3.64e-075
biogenic amine secreting cell3.64e-075
granulocytopoietic cell3.64e-075
mast cell3.64e-075
mast cell progenitor3.64e-075
basophil mast progenitor cell3.64e-075
circulating cell5.29e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.67e-4798
blood island4.67e-4798
hemolymphoid system3.59e-43108
immune system1.73e-4093
bone marrow5.76e-3976
bone element9.67e-3582
skeletal element5.24e-3090
skeletal system3.42e-25100
connective tissue8.60e-18371
lateral plate mesoderm2.27e-13203
musculoskeletal system1.18e-08167
hemopoietic organ3.60e-077
immune organ3.60e-077


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)
MA0003.10.306921
MA0004.11.38635
MA0006.10.464315
MA0007.10.260673
MA0009.10.695988
MA0014.10.636453
MA0017.10.181071
MA0019.10.403106
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.11.5214
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.10.363295
MA0040.10.620334
MA0041.10.291389
MA0042.10.264992
MA0043.10.69629
MA0046.10.685589
MA0048.10.499624
MA0050.10.73369
MA0051.10.359609
MA0052.10.623986
MA0055.10.148782
MA0056.10
MA0057.10.254521
MA0058.11.7263
MA0059.12.43567
MA0060.10.0773489
MA0061.10.0626878
MA0063.10
MA0066.10.363668
MA0067.11.00375
MA0068.11.05861
MA0069.10.681911
MA0070.10.671241
MA0071.10.329767
MA0072.10.666958
MA0073.12.01629
MA0074.10.358953
MA0076.11.79353
MA0077.10.65962
MA0078.10.447828
MA0081.10.578007
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.10.491738
MA0089.10
MA0090.10.223576
MA0091.10.278153
MA0092.10.247341
MA0093.11.46617
MA0095.10
MA0098.10
MA0100.10.979866
MA0101.10.1571
MA0103.10.146091
MA0105.10.0203556
MA0106.11.0329
MA0107.10.107387
MA0108.20.540797
MA0109.10
MA0111.10.234271
MA0113.10.414278
MA0114.10.693432
MA0115.10.929032
MA0116.10.718336
MA0117.10.732
MA0119.10.18693
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.369468
MA0139.10.453946
MA0140.10.327488
MA0141.10.197753
MA0142.10.514195
MA0143.10.414436
MA0144.10.652118
MA0145.10.324645
MA0146.10.382098
MA0147.11.75017
MA0148.10.296708
MA0149.10.319221
MA0062.21.2433
MA0035.20.872194
MA0039.21.52568
MA0138.21.13988
MA0002.20.531015
MA0137.21.54883
MA0104.21.42323
MA0047.20.388882
MA0112.20.30305
MA0065.20.333967
MA0150.10.218956
MA0151.10
MA0152.10.333125
MA0153.10.790794
MA0154.10.687815
MA0155.10.744296
MA0156.10.980055
MA0157.10.489002
MA0158.10
MA0159.10.112236
MA0160.10.30953
MA0161.10
MA0162.11.16217
MA0163.10.194919
MA0164.10.425415
MA0080.20.915505
MA0018.21.03559
MA0099.20.886817
MA0079.20.961016
MA0102.21.22472
MA0258.10.089643
MA0259.10.753086
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
BATF#1053858.699214925822730.0001707317014125790.00208306637427901
BCL11A#5333536.079168950772940.01190171164357230.0433117133817572
BCLAF1#977446.18647074574910.003132529788682840.0164492070290234
CEBPB#105184.554941500471329.08334040436614e-050.00132475211351989
E2F1#186972.453694607439660.01287341320003250.0463104988012605
E2F6#187672.508577865848690.01138806613187710.0417347967838835
EBF1#187985.089409626610864.04144399024511e-050.000739849901660314
EGR1#195882.850388054177220.00243469412076630.0137106124921121
ELF1#1997103.041498542005380.0001960883233653430.00235827595623595
ELK4#200544.638766188133720.008733913817853870.0331827722078955
ESR1#209936.593272134890250.009544258879732140.0359437780592942
FAM48A#55578182.51205357142860.01205190378031250.0437424423601063
FOS#235363.856266560954750.002556261076114450.0141442834716989
FOSL2#235544.837200172731910.007541622873992410.0310902167575943
GATA1#262376.780154071900222.55304819429845e-050.000552617202827639
GATA2#262454.551761333412140.003254844206293050.0168592309706413
GTF2F1#296254.54987888455630.003260749591375690.0168864693099462
HEY1#2346292.597214241996530.00199645482507470.0116095626657002
HSF1#3297223.47009523809520.003208762592628910.0168283597675791
IRF4#366246.261289339069750.002998943887654680.0159384611817601
JUN#372576.256414596168174.30563398722854e-050.000768151875627197
JUNB#3726510.9323688070795.80714990876497e-050.00096621463967103
JUND#372773.497331970935510.001654921271857660.0103477412866876
MAX#4149104.608968220719374.35925428810888e-060.000136596507229464
MEF2A#420545.355208831326870.005261339689734130.0243708278642898
MXI1#460164.269244983753980.001503425481111480.00960344060072182
MYC#4609103.730201336863863.09172673265338e-050.000626497571268114
NFKB1#479083.136036242396480.00127269626490260.00853522925641575
NR3C1#290844.278006666049440.01156838455163820.0422858222801532
NRF1#489954.360814088468180.003924918866440580.0191236109863395
PAX5#507994.287577841471463.71976426636989e-050.0007180932721172
POLR2A#5430142.147453176558072.25331953374171e-050.000492743799799937
POU2F2#545295.853936894263052.76328769641543e-069.56562823088933e-05
RFX5#599365.163390354512180.0005456302422474930.00471223657240436
SMARCC1#659939.356434139921030.003615975788529630.0183022630308348
SMARCC2#6601213.45076777527110.009425839501767180.0355606419725124
SMC3#912644.298552241409380.01137870676951730.0417048870433976
SP1#666793.663245171662010.0001341814525306330.00175964047223088
STAT3#677453.756951784697940.007450706951958610.030734828318019
TAL1#688636.400417859451470.01034886259116140.0384334279268299
TBP#6908123.177232017511197.62532496869237e-060.000217412316244953
TCF12#693853.798023179352290.00711439682790230.0296236540271625
USF1#739173.180749638603980.002913753057932640.0157453021998979
USF2#739254.640070494667710.002991628438887930.0159036283482142
YY1#752872.455585374926930.01281875463892510.046117048423517



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C616&oldid=3067733"