Personal tools

Coexpression cluster:C898: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(4 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Coexpression_clusters
{
|full_id=C898_CD14_Mast_Basophils_Natural_CD19_immature_CD8
|

Latest revision as of 11:33, 17 September 2013


Full id: C898_CD14_Mast_Basophils_Natural_CD19_immature_CD8



Phase1 CAGE Peaks

Hg19::chr12:7052974..7052985,+p1@RNU7-1
p4@C12orf57
Hg19::chr14:35343199..35343210,-p@chr14:35343199..35343210
-
Hg19::chr17:56736656..56736674,-p1@ENST00000365207
Hg19::chr19:49382363..49382367,+p@chr19:49382363..49382367
+
Hg19::chr19:49383883..49383887,+p@chr19:49383883..49383887
+
Hg19::chr2:157189617..157189667,-p4@NR4A2
Hg19::chr2:224702739..224702758,+p@chr2:224702739..224702758
+
Hg19::chr8:81397820..81397836,+p2@ZBTB10
Hg19::chrX:139014487..139014499,+p@chrX:139014487..139014499
+


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

GO IDGO nameFDR corrected p-value
GO:0042053regulation of dopamine metabolic process0.0100078001646933
GO:0042069regulation of catecholamine metabolic process0.0100078001646933
GO:0042417dopamine metabolic process0.0183457432124587
GO:0006584catecholamine metabolic process0.0266764682822135
GO:0018958phenol metabolic process0.0266764682822135
GO:0042133neurotransmitter metabolic process0.0266764682822135
GO:0006576biogenic amine metabolic process0.0450359718763971
GO:0001505regulation of neurotransmitter levels0.0450359718763971
GO:0006575amino acid derivative metabolic process0.0450359718763971
GO:0003707steroid hormone receptor activity0.0450359718763971
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0450359718763971
GO:0004879ligand-dependent nuclear receptor activity0.0450359718763971
GO:0006355regulation of transcription, DNA-dependent0.0450359718763971
GO:0006351transcription, DNA-dependent0.0450359718763971
GO:0032774RNA biosynthetic process0.0450359718763971
GO:0003677DNA binding0.0450359718763971
GO:0006725aromatic compound metabolic process0.0450359718763971
GO:0045449regulation of transcription0.0450359718763971
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0450359718763971
GO:0030182neuron differentiation0.0450359718763971
GO:0006350transcription0.0450359718763971
GO:0010468regulation of gene expression0.0450359718763971
GO:0045893positive regulation of transcription, DNA-dependent0.0450359718763971
GO:0031323regulation of cellular metabolic process0.0450359718763971
GO:0048699generation of neurons0.0450359718763971
GO:0019222regulation of metabolic process0.0450359718763971
GO:0016070RNA metabolic process0.0450359718763971
GO:0008270zinc ion binding0.0450359718763971
GO:0022008neurogenesis0.0450359718763971
GO:0045941positive regulation of transcription0.0451569455497714
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0451569455497714
GO:0007268synaptic transmission0.0451569455497714
GO:0019226transmission of nerve impulse0.049798892575355



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
classical monocyte3.93e-5042
CD14-positive, CD16-negative classical monocyte3.93e-5042
leukocyte2.24e-49136
defensive cell9.01e-4248
phagocyte9.01e-4248
hematopoietic lineage restricted progenitor cell9.53e-39120
hematopoietic stem cell1.00e-38168
angioblastic mesenchymal cell1.00e-38168
myeloid leukocyte1.85e-3872
nongranular leukocyte4.06e-38115
hematopoietic cell2.65e-37177
granulocyte monocyte progenitor cell3.43e-3567
macrophage dendritic cell progenitor5.10e-3461
hematopoietic oligopotent progenitor cell5.19e-34161
hematopoietic multipotent progenitor cell5.19e-34161
myeloid lineage restricted progenitor cell2.51e-3266
monopoietic cell6.83e-3259
monocyte6.83e-3259
monoblast6.83e-3259
promonocyte6.83e-3259
myeloid cell6.83e-27108
common myeloid progenitor6.83e-27108
stuff accumulating cell2.46e-2087
intermediate monocyte1.36e-119
CD14-positive, CD16-positive monocyte1.36e-119
mesenchymal cell1.12e-10354
connective tissue cell5.77e-10361
motile cell2.81e-08386
lymphoid lineage restricted progenitor cell2.09e-0752
lymphocyte3.80e-0753
common lymphoid progenitor3.80e-0753
Uber Anatomy
Ontology termp-valuen
bone marrow1.69e-3076
hematopoietic system3.98e-3098
blood island3.98e-3098
bone element5.39e-2782
immune system4.55e-2693
hemolymphoid system1.68e-25108
skeletal element4.42e-2390
skeletal system4.06e-19100
connective tissue3.09e-10371
lateral plate mesoderm2.31e-08203


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)
MA0003.11.0633
MA0004.10.415381
MA0006.10.733408
MA0007.10.397529
MA0009.10.870971
MA0014.10.367355
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.559235
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.10.693769
MA0056.10
MA0057.10.539841
MA0058.10.325084
MA0059.10.865474
MA0060.10.488252
MA0061.14.21471
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.11.73295
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.11.46949
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.12.03788
MA0084.11.37471
MA0087.10.838229
MA0088.10.363555
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.11.36936
MA0103.10.714036
MA0105.13.65227
MA0106.10.554855
MA0107.12.48064
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.11.51455
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.12.07572
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.706237
MA0146.10.0794051
MA0147.10.607251
MA0148.11.11902
MA0149.10.464973
MA0062.20.421263
MA0035.21.19307
MA0039.20.323611
MA0138.20.608783
MA0002.20.152495
MA0137.20.28622
MA0104.20.486672
MA0047.22.30237
MA0112.20.674448
MA0065.20.182082
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.225151
MA0155.10.645215
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.502732
MA0163.10.101664
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.22.11589
MA0102.21.41188
MA0258.10.532421
MA0259.10.624802
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
BCL3#602311.51570093457940.001785915017827760.0109562487398328
BCLAF1#977437.217549203373950.00670404961947760.028501353016715
BRF2#552901119.3972868217050.008344470633487870.0328565890699306
FOXA2#317038.210154584221750.00467281236756890.0220535880905838
GATA1#262357.533504524333580.0002132601043529180.00245835232213184
HDAC2#306645.9624978829450.002864271980786230.0155228945774134
HEY1#2346273.142308589082220.001258763462843770.0084586280591906
MAFK#797539.033577712609970.003567854712813750.0180832368412868
MEF2A#420536.247743636548020.01000005008462560.037498033562696
NFKB1#479063.658708949462560.001850649648602720.0109346005120174
PAX5#507953.705314183987680.005616557077719420.0253912044255882
POLR2A#543092.147453176558070.001029412892608020.00728640142941982
POU2F2#545244.047166247885570.01161426156153230.042435693507727
REST#597844.288901651612450.009457025945962830.0356654148257831
SIN3A#2594253.004935959341740.01401618817346520.0491963258829957
SIRT6#51548351.21280133000832.24384938017015e-050.000490775676263016
STAT1#677236.902195832399730.007591561082166650.0312874412162268
STAT2#6773214.50306026365350.007865683132259650.0322973886632619
TCF7L2#693444.786745139172150.006382053991234720.0277827242211897
TRIM28#1015536.196841681754170.0102278065029780.0380840660070064
ZBTB33#10009310.55490834332710.002291721628821160.0130043529036921
ZEB1#693535.629477339181290.01330488236341950.0470363756398743



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:C898&oldid=3068015"