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Coexpression cluster:C3231

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Full id: C3231_lymphangiectasia_Whole_CD4_Neutrophils_CD14_Eosinophils_migratory



Phase1 CAGE Peaks

Hg19::chr12:109027545..109027622,-p1@SELPLG
Hg19::chr12:109027626..109027638,-p3@SELPLG
Hg19::chr12:109027643..109027677,-p2@SELPLG


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 cell4.17e-77172
angioblastic mesenchymal cell4.17e-77172
hematopoietic oligopotent progenitor cell6.20e-73165
hematopoietic multipotent progenitor cell6.20e-73165
hematopoietic cell1.48e-71182
leukocyte1.02e-64140
hematopoietic lineage restricted progenitor cell5.49e-53124
nongranular leukocyte2.28e-51119
myeloid cell5.55e-50112
common myeloid progenitor5.55e-50112
myeloid leukocyte2.52e-3776
granulocyte monocyte progenitor cell2.61e-3271
myeloid lineage restricted progenitor cell8.76e-3270
macrophage dendritic cell progenitor7.39e-3065
monopoietic cell3.17e-2963
monocyte3.17e-2963
monoblast3.17e-2963
promonocyte3.17e-2963
CD14-positive, CD16-negative classical monocyte6.11e-2442
classical monocyte5.85e-2345
lymphoid lineage restricted progenitor cell5.47e-1952
lymphocyte5.78e-1953
common lymphoid progenitor5.78e-1953
T cell1.01e-1425
pro-T cell1.01e-1425
mesenchymal cell4.60e-12358
mature alpha-beta T cell6.25e-1218
alpha-beta T cell6.25e-1218
immature T cell6.25e-1218
mature T cell6.25e-1218
immature alpha-beta T cell6.25e-1218
connective tissue cell8.40e-11365
CD8-positive, alpha-beta T cell3.11e-0811
motile cell2.82e-07390
dendritic cell2.95e-0710
intermediate monocyte3.34e-079
CD14-positive, CD16-positive monocyte3.34e-079
granulocyte4.33e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.42e-40102
blood island6.42e-40102
hemolymphoid system1.85e-35112
adult organism7.01e-28115
bone marrow7.18e-2880
bone element6.76e-2686
immune system1.48e-20115
skeletal element5.11e-20101
skeletal system5.11e-20101
connective tissue1.81e-09375
neural tube1.95e-0957
neural rod1.95e-0957
future spinal cord1.95e-0957
neural keel1.95e-0957
blood2.39e-0915
haemolymphatic fluid2.39e-0915
organism substance2.39e-0915
anterior neural tube1.93e-0842
regional part of forebrain2.69e-0841
forebrain2.69e-0841
future forebrain2.69e-0841
telencephalon4.23e-0734
gray matter6.05e-0734
brain grey matter6.05e-0734
regional part of telencephalon7.53e-0733
Disease
Ontology termp-valuen
hematologic cancer2.18e-1351
immune system cancer2.18e-1351
leukemia3.67e-1339
myeloid leukemia9.39e-1131


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
BCL11A#53335328.36945510360714.37778126761649e-050.000776777264370707
BCL3#602334.54710280373832.42397750207122e-050.000526534497376906
CHD2#1106310.34402283411690.0009033701102746880.0065875625573927
CTCF#1066435.360256373075030.0064925092527670.0278537287976394
EBF1#187938.9064668465690.00141523283560980.00912774051245923
EGR1#195834.988179094810140.008056488137383440.0319321276880527
ELF1#199734.258097958807540.01295179875054610.0460390357614881
GATA1#2623313.56030814380040.0004009615963782630.00387024289871991
IRF4#3662321.91451268674419.49854535978121e-050.00136210157741342
MAX#414936.452555509007120.003721913834265510.018591589771229
MYC#460935.22228187160940.007020843755740150.0293405586413407
NFKB1#479035.488063424193840.006049381815655430.0268755907540088
PAX5#507936.669565531177830.003370290999677260.0172434145747952
POU2F2#545239.106124057742520.001324165192682130.00879959840662566
SP1#666735.69838137814090.005403962701712170.0245619488469021
SPI1#668838.204323508522730.001810593189410520.0108845071149971
SRF#6722313.79717826216780.0003806615025800190.00374067620135064
TCF12#6938310.63446490218640.0008313523990202070.00627987944461676
USF1#739136.361499277207960.00388404057290560.0189651369112015
USF2#7392312.99219738506960.0004558979393427810.0042061417744718
YY1#752834.911170749853860.008441455341808260.0328177916335286
ZEB1#6935316.88843201754390.0002075486917327580.00242164873375908



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.