Personal tools

Coexpression cluster:C413

From FANTOM5_SSTAR

Revision as of 17:11, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C413_CD14_Smooth_gall_mesothelioma_meningioma_Fibroblast_Neutrophils



Phase1 CAGE Peaks

Hg19::chr11:4414880..4414953,-p1@TRIM21
Hg19::chr11:5711010..5711105,+p1@TRIM22
Hg19::chr11:615570..615721,-p2@IRF7
Hg19::chr12:113344755..113344805,+p1@OAS1
Hg19::chr12:113376261..113376324,+p1@OAS3
Hg19::chr12:113376330..113376350,+p3@OAS3
Hg19::chr12:113416191..113416202,+p6@OAS2
Hg19::chr12:113416240..113416251,+p5@OAS2
Hg19::chr12:113416265..113416287,+p3@OAS2
Hg19::chr12:113416311..113416336,+p2@OAS2
Hg19::chr12:113416340..113416363,+p4@OAS2
Hg19::chr12:113416367..113416393,+p1@OAS2
Hg19::chr14:24630902..24630948,+p2@IRF9
Hg19::chr17:4847640..4847689,+p@chr17:4847640..4847689
+
Hg19::chr17:6659354..6659398,+p1@XAF1
Hg19::chr19:17516624..17516640,+p3@FAM125A
Hg19::chr20:62205570..62205609,-p1@PRIC285
Hg19::chr21:42798158..42798174,+p1@MX1
Hg19::chr2:37384085..37384134,-p1@EIF2AK2
Hg19::chr2:7005785..7005864,-p1@CMPK2
Hg19::chr3:122283100..122283153,-p1@PARP9
Hg19::chr3:122399656..122399694,+p1@PARP14
Hg19::chr3:146262365..146262412,-p1@PLSCR1
Hg19::chr3:187086155..187086211,+p1@RTP4
Hg19::chr9:32526172..32526181,-p3@DDX58


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
1.37766611460316e-122.90687550181267e-107135Hepatitis C (KEGG):05160
8.02404527164351e-155.07922065695034e-128134Measles (KEGG):05162
7.38492015576474e-142.33732722929954e-118176Influenza A (KEGG):05164
4.05004898661881e-060.000512736201705942350Type II interferon signaling (IFNG) (Wikipathways):WP619
3.73290025145396e-105.90731464792589e-088511Signaling in Immune system (Reactome):REACT_6900



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:0009615response to virus1.85714517836697e-14
GO:0051707response to other organism4.03157118129478e-12
GO:0009607response to biotic stimulus4.11531196650602e-11
GO:0051704multi-organism process9.61507303276969e-11
GO:0003723RNA binding1.04948661341494e-05
GO:0005792microsome0.0024331112221386
GO:0042598vesicular fraction0.0024331112221386
GO:0003950NAD+ ADP-ribosyltransferase activity0.00417910917080701
GO:0005634nucleus0.00417910917080701
GO:0016779nucleotidyltransferase activity0.00417910917080701
GO:0006955immune response0.00449250958849504
GO:0003676nucleic acid binding0.00519863380303236
GO:0002376immune system process0.00772038312651502
GO:0016763transferase activity, transferring pentosyl groups0.0113341044691317
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0121968044765909
GO:0032553ribonucleotide binding0.0121968044765909
GO:0032555purine ribonucleotide binding0.0121968044765909
GO:0005737cytoplasm0.0133518821572491
GO:0017076purine nucleotide binding0.0136007388506822
GO:0005524ATP binding0.017442046567622
GO:0032559adenyl ribonucleotide binding0.017442046567622
GO:0017128phospholipid scramblase activity0.017442046567622
GO:0004694eukaryotic translation initiation factor 2alpha kinase activity0.017442046567622
GO:0017121phospholipid scrambling0.017442046567622
GO:0006926virus-infected cell apoptosis0.017442046567622
GO:0030554adenyl nucleotide binding0.0185944180558335
GO:0001580detection of chemical stimulus during sensory perception of bitter taste0.020182800670166
GO:0044424intracellular part0.0207146498389662
GO:0050913sensory perception of bitter taste0.0218595978581463
GO:0000166nucleotide binding0.0218595978581463
GO:0005622intracellular0.0221159790034413
GO:0050912detection of chemical stimulus during sensory perception of taste0.0231075963630502
GO:0050907detection of chemical stimulus during sensory perception0.0231075963630502
GO:0016740transferase activity0.0241057480557124
GO:0032606interferon type I production0.0241057480557124
GO:0045351interferon type I biosynthetic process0.0241057480557124
GO:0043231intracellular membrane-bound organelle0.0241057480557124
GO:0043227membrane-bound organelle0.0241057480557124
GO:0006355regulation of transcription, DNA-dependent0.0242975136235004
GO:0005624membrane fraction0.0242975136235004
GO:0006351transcription, DNA-dependent0.0258731915644999
GO:0032774RNA biosynthetic process0.0258731915644999
GO:0007009plasma membrane organization and biogenesis0.0321401529072117
GO:0030968unfolded protein response0.0321401529072117
GO:0045449regulation of transcription0.0323666252050385
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0342513187993206
GO:0006350transcription0.0375499264667628
GO:0004386helicase activity0.0375499264667628
GO:0010468regulation of gene expression0.0375499264667628
GO:0009593detection of chemical stimulus0.0391154881512025
GO:0031323regulation of cellular metabolic process0.0402711693658135
GO:0000267cell fraction0.0402711693658135
GO:0003712transcription cofactor activity0.0403451482669919
GO:0065007biological regulation0.0414568524609404
GO:0006984ER-nuclear signaling pathway0.0414568524609404
GO:0019222regulation of metabolic process0.0467566200919185
GO:0016070RNA metabolic process0.0467566200919185
GO:0030168platelet activation0.0467566200919185
GO:0017111nucleoside-triphosphatase activity0.0470607886633734



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
leukocyte4.22e-38140
nongranular leukocyte7.38e-36119
hematopoietic lineage restricted progenitor cell3.68e-33124
hematopoietic stem cell2.68e-28172
angioblastic mesenchymal cell2.68e-28172
hematopoietic oligopotent progenitor cell1.04e-26165
hematopoietic multipotent progenitor cell1.04e-26165
myeloid leukocyte3.96e-2676
hematopoietic cell5.71e-25182
CD14-positive, CD16-negative classical monocyte5.93e-2442
monopoietic cell1.36e-2263
monocyte1.36e-2263
monoblast1.36e-2263
promonocyte1.36e-2263
macrophage dendritic cell progenitor1.17e-2165
myeloid lineage restricted progenitor cell1.52e-2170
granulocyte monocyte progenitor cell1.58e-2171
classical monocyte5.13e-2145
myeloid cell1.65e-14112
common myeloid progenitor1.65e-14112
lymphoid lineage restricted progenitor cell3.65e-1252
lymphocyte4.28e-1253
common lymphoid progenitor4.28e-1253
lymphocyte of B lineage4.65e-0724
pro-B cell4.65e-0724
Uber Anatomy
Ontology termp-valuen
hemolymphoid system7.53e-27112
hematopoietic system1.46e-26102
blood island1.46e-26102
bone marrow4.08e-1980
immune system2.36e-16115
bone element7.72e-1586
skeletal element2.46e-13101
skeletal system2.46e-13101
lateral plate mesoderm4.35e-08216
adult organism8.45e-07115


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
EBF1#1879134.631362760215886.26618592042133e-072.86279173815785e-05
EGR1#1958132.593853129301270.000377785726401510.00374696709208427
ELF1#1997132.214210938579920.001847705895137980.0109277170837712
HEY1#23462142.26246218413920.0008220701032371530.00625910764102829
IRF1#365992.7493789512830.003181199298650190.0166980586797873
IRF4#366265.259483044818590.0007529204584399410.0059266098702901
NFKB1#4790224.829495813290576.96316904821618e-141.10688951632671e-11
POLR2A#5430252.147453176558075.02456472262233e-094.04283909912137e-07
POU2F2#5452145.099429472335815.03322093134357e-083.21901139527613e-06
SPI1#668892.953556463068180.001926757153081220.0113246997754882
STAT1#67722319.05006049742331.42509837352088e-285.29664943174902e-26
STAT2#67732360.04266949152544.88212981441461e-402.8326930871536e-37
STAT3#6774104.20778599886175.1112914742446e-050.000870544961315446
SUZ12#2351236.013893709327550.01315455203308180.0466391098816253
TAF1#6872212.808158880026053.24290519342898e-082.18084852219272e-06
TBP#6908202.965416549677115.02099441389296e-083.2131595318172e-06
YY1#7528163.143149279906472.64335913146096e-069.267196519995e-05
ZBTB33#1000945.066356004796980.007391990141568670.0305469100777624



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.