Personal tools

Coexpression cluster:C3602: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
Line 1: Line 1:
{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 12:29, 17 September 2013


Full id: C3602_Mast_chronic_leukemia_hairy_acute_biphenotypic_CD14CD16



Phase1 CAGE Peaks

Hg19::chr16:89043500..89043528,-p3@CBFA2T3
Hg19::chr16:89043559..89043601,-p4@CBFA2T3
Hg19::chr16:89043605..89043625,-p6@CBFA2T3


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 cell1.18e-63168
angioblastic mesenchymal cell1.18e-63168
hematopoietic oligopotent progenitor cell6.10e-59161
hematopoietic multipotent progenitor cell6.10e-59161
hematopoietic cell1.61e-58177
myeloid cell2.11e-54108
common myeloid progenitor2.11e-54108
leukocyte3.42e-33136
hematopoietic lineage restricted progenitor cell3.59e-32120
nongranular leukocyte9.35e-30115
myeloid lineage restricted progenitor cell1.70e-2966
granulocyte monocyte progenitor cell2.02e-2767
myeloid leukocyte4.20e-2772
monopoietic cell1.19e-2259
monocyte1.19e-2259
monoblast1.19e-2259
promonocyte1.19e-2259
macrophage dendritic cell progenitor1.84e-2161
classical monocyte9.45e-2042
CD14-positive, CD16-negative classical monocyte9.45e-2042
defensive cell3.39e-1848
phagocyte3.39e-1848
lymphocyte of B lineage6.05e-1424
pro-B cell6.05e-1424
mesenchymal cell9.21e-13354
connective tissue cell6.13e-12361
intermediate monocyte8.23e-119
CD14-positive, CD16-positive monocyte8.23e-119
B cell3.69e-1014
motile cell3.97e-09386
nucleate cell5.52e-0855
histamine secreting cell6.26e-085
biogenic amine secreting cell6.26e-085
granulocytopoietic cell6.26e-085
mast cell6.26e-085
mast cell progenitor6.26e-085
basophil mast progenitor cell6.26e-085
lymphocyte5.61e-0753
common lymphoid progenitor5.61e-0753
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.04e-3298
blood island2.04e-3298
hemolymphoid system5.71e-30108
bone marrow2.13e-2376
immune system5.96e-2393
bone element1.60e-2082
skeletal element2.54e-1790
adult organism1.47e-14114
skeletal system4.20e-14100
connective tissue3.21e-11371
lateral plate mesoderm2.04e-09203
blood2.93e-0815
haemolymphatic fluid2.93e-0815
organism substance2.93e-0815
Disease
Ontology termp-valuen
myeloid leukemia2.27e-3531
leukemia1.65e-3139
hematologic cancer7.06e-2451
immune system cancer7.06e-2451
chronic leukemia6.84e-098


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)
MA0003.19.41405
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
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
MA0051.12.15619
MA0052.11.24796
MA0055.11.06172
MA0056.10
MA0057.10.333427
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
MA0073.10.211629
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
MA0089.10
MA0090.10.751469
MA0091.11.93651
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.11.55947
MA0103.10.628063
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
MA0116.10.560723
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
MA0139.10.440097
MA0140.12.07172
MA0141.11.6959
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.11.37817
MA0146.14.51393
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.15986
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.05956
MA0163.10.122425
MA0164.11.01792
MA0080.22.62633
MA0018.22.26143
MA0099.20.902716
MA0079.20.0373086
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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#90536.336201576962630.003930750035764890.0189784847203203
E2F6#187635.017155731697390.00791769806886330.0321582199818781
EBF1#187938.9064668465690.00141523283560980.0091435510125736
EGR1#195834.988179094810140.008056488137383440.0320110924321929
ELF1#199734.258097958807540.01295179875054610.0461537092161964
ETS1#211339.728760922202340.001085840092584840.00761305407018446
GABPB1#255337.067683836182170.002832212825417420.0153914806573926
GATA1#2623313.56030814380040.0004009615963782630.00387525709459091
GATA2#2624312.7449317335540.0004829527704283790.0043674001550584
HDAC2#3066313.41562023662630.0004140761399857210.0039079792141667
HMGN3#932438.178547723350590.001827766942164210.0108608415835622
MAX#414936.452555509007120.003721913834265510.0186299045740165
MXI1#460139.96157162875930.001011470541259020.00719548885352163
MYC#460935.22228187160940.007020843755740150.0294099912163383
NFKB1#479035.488063424193840.006049381815655430.0269294312878922
PAX5#507936.669565531177830.003370290999677260.017272183213862
PBX3#5090321.91451268674419.49854535978121e-050.00136472496743732
REST#597839.650028716128020.001112636247114590.00766760917270872
SIN3A#2594235.408884726815140.006318961977991520.0276232083219395
SPI1#668838.204323508522730.001810593189410520.0108995643615681
TAL1#6886329.86861667744023.75103522793067e-050.00071947542363609
TCF12#6938310.63446490218640.0008313523990202070.00628761048600705
USF1#739136.361499277207960.00388404057290560.0190024506204004
YY1#752834.911170749853860.008441455341808260.0328851189691191
ZBTB7A#5134137.35190930787590.002516255860282270.0139970836640223



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:C3602&oldid=3070719"