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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0.0115458124038492,0.00510832569441125,0,0,0,0,0,0.0486190497334647,0,0,0,0,0.0644233438457899,0,0,-0.0322859259446875,0,0,0,0,0,0,0,0,0.108243180411789,0.0956232112328326,0.138444965523214,0.69419734522523,0.518905469136572,0.50070643982006,0,0,0,0.032404058578668,0.056519526161287,0.389001225196897,0.815574699308565,0.716957191770421,0.582193099729728,0.0355914623208881,0.184615233793662,0,0.438507361017538,0.276958704279243,0.185321487128486,0.419460611453034,0.500179197804137,0.456098423073655,0.701368793562642,0.66145771448084,0.775692481337067,0.615825813067911,0.467823209448954,0.608004945024432,0.460912146915908,0.259765472565373,0.480367941816861,0.637310478542302,0.713665011430876,0.63570447139197,0.365376626635383,0.446408679939277,0.495700232751619,0.704401866333175,0.431710365575549,0.643791382810284,0.478564954935613,0.408994025090247,0.650795127684496,0.344549260502074,0.704845304255587,0.782232762319557,0.355553370616496,0.543347062022495,0.493877013625811,0.640467417518994,0.470160428705896,0.552038433218784,0.432981544287895,0.413523295697036,0.418984810704378,0.798977960984417,0.697616285969516,0.749727548904464,0.357971163872208,0.826831488417386,0.790480233143864,0.775830220040148,0.6827058675994,0.625225047844876,0.33735429485416,0.402964784522434,0.695931486150419,0.510817598835734,0.183773097089987,0.343737480523169,0.472032579926512,0.402747901480023,0.231570778466396,0.658889950809016,0.634893694906244,0.469566853250347,0.198229100002757,0.493645654881607,0.410549780545484,0.547596784982932,0.12267799803443,0.143070424715714,0.123484395618314,0.262225590440628,0.21954442557803,0.411671183306063,0.46468889535634,0.437898360826898,0.0792683493713273,0.556982197269714,0.375573963022984,0.251485014926523,0.381487626557256,0.362136806900612,0.553327753570124,0.343329990739072,0.433067054433216,0.299888822692479,0.47518278558175,0.559192528178062,0.507542064946755,0.415747901692709,0.437416447069061,0,0,-0.0322859259446875,0,0,0,0,0,0,0,0,0.0051924762192805,-0.0322859259446875,0,0,0,0,0.238756260583255,0.594436796152995,0.456873784329295,0.070734612273697,0,0,0.0512928890093658,0,0.0328415566152558,0.0789643135049952,0,0,0,0,0,0,0.0632702893228914,0,0.0192062731316619,0,0,0.229788186321734,0.237711068461351,0.0208988377175442,1.10924899145442,1.06923459350541,0,-0.0322859259446875,0,0.147934180290477,0,0,0,0,0,0,0,0,0,0,0,-0.0322859259446875,0,-0.0322859259446875,0,0,0,0,0,0,0,0,0,0.162470557806361,0,0,0,0,0,0,0,0,0,0.0107693832624117,0,0.0425961947748989,0.0473965650227375,0.0233325146134975,0,0,0.0654688447297279,0.0382424828832804,0,0,0.0540007547494703,0,0,-0.00581674989452907,-0.0322859259446875,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0226453828266747,0,0.0892105187786361,0.0143904430276994,0,0,0,-0.0238577890677405,0,-0.0322859259446875,0,0,-0.0322859259446875,0,0,0,-0.0322859259446875,-0.0170768118249852,-0.0322859259446875,0,0,-0.0322859259446875,0,0,0.04335377925284,0.220616693771521,0,0,0,0,0,0,0,0,0,0,0.173961836914205,0.0695110690833982,0.483668581925074,0.43607346291025,0.482575653980327,0,0,0.264185871351927,0,0,0,0,0,0,-0.00154930508676611,0,0,-0.0322859259446875,0,0,0,0,0,0,0,0.060997624489797,-0.0322859259446875,-0.0322859259446875,-0.0322859259446875,0,0,0,0,0,-0.0322859259446875,0,0,0,0,0,0,-0.00602192420146808,0.545037187688657,0.580144422332684,0.685767803404128,0,0,0,0,0.0850474338274186,0.888800614032242,0.811770369532987,1.16659917878408,0,0,-0.00717951502425584,0,0,0,0,-0.0322859259446875,0,0,0,0.0412011673804016,0,0.091355179141637,0,0.298205949268248,0.648499276463506,0.465545836041337,0,0,0.0699621070195304,0,0.0435414814425919,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.0322859259446875,0,0,0.0520997348758331,-0.0322859259446875,0,0,0,0,-0.0322859259446875,0,0,0,0,0,-0.0322859259446875,0.0442716305375648,0.0380513783661453,0.0511552149920212,0,0,-0.0322859259446875,0.0584338389878518,0,0.024569531247964,0,0,0.00665185519099692,0,0,0,0,0,0,-0.0322859259446875,0,0.229691380353826,0,0,0,0,0,0,0,0,0,0,0.0678224139834436,0.199465760932502,0,0,0,0,0,-0.0322859259446875,0,0,0,0,0.00527997164546413,0,0,0,0,0,0,0.00752443725486199,0.0650528139794752,0.107784894264258,0,-0.0322859259446875,0,0.0797027431157969,0,0,0,0.0980268415704232,0,0,0,0.0227616023906395,0,0,0,-0.0322859259446875,0.401804113981,0.33028711668548,0.195802046114694,0.136936804170074,0.390213482665224,0.328864977011411,0.418316924266286,0.240981690857942,-0.0080813678061641,-0.0322859259446875,-0.0134498022624084,0,0.0063682498473685,0,-0.0322859259446875,0.0731581564665672,0.124438274574311,0.0806020066999317,0,0.0553203986812641,0,0,0,0,0.0646781039303325,0.0475461679201446,0,0,0,0,0.04685108239435,0.0775089264793031,0,-0.0322859259446875,0,0,-0.0322859259446875,-0.0322859259446875,0,0,0.0873862460237173,0,0,0,0,0,0,0,0.0662528064680222,0,0.0935012578545402,0,0,0,0.0181266256446274,-0.0322859259446875,-0.0147859221598055,0,0.127268981541051,0,0.383238471017613,0,0,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|full_id=C875_Eosinophils_Neutrophils_Mast_CD19_CD14_Basophils_Peripheral
|full_id=C875_Eosinophils_Neutrophils_Mast_CD19_CD14_Basophils_Peripheral
|id=C875
|id=C875

Revision as of 18:38, 12 September 2012


Full id: C875_Eosinophils_Neutrophils_Mast_CD19_CD14_Basophils_Peripheral



Phase1 CAGE Peaks

Hg19::chr10:70660801..70660814,-p@chr10:70660801..70660814
-
Hg19::chr11:102187888..102187900,-p@chr11:102187888..102187900
-
Hg19::chr19:2270812..2270826,-p@chr19:2270812..2270826
-
Hg19::chr1:225655463..225655481,-p@chr1:225655463..225655481
-
Hg19::chr1:66801524..66801541,-p@chr1:66801524..66801541
-
Hg19::chr20:34330506..34330528,+p@chr20:34330506..34330528
+
Hg19::chr20:34330534..34330580,+p@chr20:34330534..34330580
+
Hg19::chr2:208031542..208031595,-p2@KLF7
Hg19::chr5:130971280..130971333,+p@chr5:130971280..130971333
+


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
leukocyte6.15e-42140
hematopoietic cell2.60e-34182
hematopoietic stem cell3.60e-33172
angioblastic mesenchymal cell3.60e-33172
hematopoietic lineage restricted progenitor cell4.96e-32124
nongranular leukocyte1.20e-30119
hematopoietic oligopotent progenitor cell7.40e-30165
hematopoietic multipotent progenitor cell7.40e-30165
CD14-positive, CD16-negative classical monocyte2.26e-2442
multi fate stem cell1.62e-23430
stem cell1.70e-23444
somatic stem cell7.94e-23436
connective tissue cell3.23e-22365
mesenchymal cell8.32e-22358
myeloid leukocyte9.77e-2276
classical monocyte2.85e-2145
motile cell5.27e-19390
granulocyte monocyte progenitor cell3.28e-1871
native cell1.95e-17722
myeloid lineage restricted progenitor cell1.32e-1670
macrophage dendritic cell progenitor7.82e-1665
myeloid cell1.35e-15112
common myeloid progenitor1.35e-15112
monopoietic cell5.69e-1563
monocyte5.69e-1563
monoblast5.69e-1563
promonocyte5.69e-1563
lymphoid lineage restricted progenitor cell3.12e-1452
lymphocyte4.29e-1453
common lymphoid progenitor4.29e-1453
somatic cell2.90e-13591
mature alpha-beta T cell1.06e-0818
alpha-beta T cell1.06e-0818
immature T cell1.06e-0818
mature T cell1.06e-0818
immature alpha-beta T cell1.06e-0818
B cell6.00e-0814
T cell1.23e-0725
pro-T cell1.23e-0725
animal cell9.91e-07679
eukaryotic cell9.91e-07679
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.15e-24102
blood island2.15e-24102
hemolymphoid system1.27e-23112
connective tissue1.78e-20375
bone marrow9.39e-1880
bone element2.29e-1586
immune system7.88e-15115
lateral plate mesoderm1.39e-14216
skeletal element3.52e-12101
skeletal system3.52e-12101
musculoskeletal system6.03e-08167
blood3.64e-0715
haemolymphatic fluid3.64e-0715
organism substance3.64e-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)

{{{tfbs_overrepresentation_jaspar}}}



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
BCL3#602311.51570093457940.001785915017827760.0109549617377489
BRCA1#67248.970769174766120.0006202690356731910.00514006806448245
CHD2#110666.896015222744575.28898897155739e-050.00089758972895756
CTCF#1066463.573504248716680.002103883629372150.0121645076879809
E2F4#187445.630249029015310.003536571815964610.017945584680183
E2F6#187663.344770487798260.003009555364094890.0159842835979814
EBF1#187965.937644564379340.0001242436507924170.00165593193531256
EGR1#195863.325452729873420.003104936414383980.016325653435123
ELF1#199794.258097958807542.17161853202127e-067.82074716778515e-05
FOS#235354.998864060496890.001450289921505040.00929757713535482
FOSL2#235535.643400201520560.01321558041905920.0467570718312314
FOXA1#316944.925075444171310.005758150542003090.0259280626220687
FOXA2#317038.210154584221750.00467281236756890.0220515950863734
GABPB1#255353.926491020101210.004337976092287310.0205830668803051
GATA1#262346.026803619466860.002753144894242950.0151000787527486
GTF2F1#296245.662071500781180.00346420020706550.0176022966539707
HEY1#2346273.142308589082220.001258763462843770.0084564516464647
IRF3#3661315.66065073716320.0007351478720625020.00579282545724579
IRF4#3662512.17472927041342.1331797509613e-050.000470015105507695
MAFF#23764212.51452366443230.01044482063014860.0386975991270384
MAX#414975.018654284783325.77474544696214e-050.000962202679858454
MXI1#460155.534206460421830.000906612702046980.00660152854975141
MYC#460963.48152124773960.002423669811459260.0136544207271007
NFKB1#479063.658708949462560.001850649648602720.0109333634263163
NFYA#480036.141860233276840.01048163163058090.0388147050266368
NFYB#480135.586597751178820.01358500277111940.047947149620254
NRF1#489956.783488582061620.0003500419849025880.00352400567391955
PAX5#507985.928502694380291.99061202941177e-067.30233683666089e-05
POLR2A#543092.147453176558070.001029412892608020.00728393313625267
POU2F2#545277.082540933799745.66141070992737e-060.000170444529586078
REST#597855.361127064515570.001050372213652920.00742368705567415
RFX5#599345.354627034308930.004249445027674740.0202199548610562
RXRA#625636.691539046377760.008273246622947750.0325958051929244
SIN3A#2594263.605923151210090.002003057991334320.0116453670428059
SP1#666763.79892091876060.001506997871138380.00962390550714326
SP2#666838.71784349794820.003945531750578630.0189430143198033
SPI1#668887.292732007575763.90517100687164e-071.89786949644796e-05
SRF#672246.132079227630140.002582573603250730.0142860913426856
STAT1#677236.902195832399730.007591561082166650.0312862066080184
TAF1#687293.343046285745291.91655056102793e-050.000433440069387606
TBP#690883.294907277419010.0001918853220272470.00231492562633749
TCF12#693867.089643268124284.5123563262149e-050.000793777972635268
TCF7L2#693455.983431423965190.0006305154397321440.00518384649375623
TFAP2A#702035.506211457681650.01413162662770550.0495848464092368
TFAP2C#702244.804101604382320.006299303434747120.0277849882347138
TRIM28#1015548.262455575672230.0008469285971791930.00638368762707836
USF2#739245.774309948919820.003223241005374920.0166996759281849
YY1#752873.819799472108550.0003529672812141940.00353573277217813
ZBTB33#10009310.55490834332710.002291721628821160.0130036463757716



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.