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Coexpression cluster:C1768

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Full id: C1768_testis_CD8_Natural_embryonic_Eosinophils_CD4_CD14



Phase1 CAGE Peaks

  Short description
Hg19::chr16:85833874..85833901,+ p@chr16:85833874..85833901
+
Hg19::chr1:114471972..114472000,+ p3@HIPK1
Hg19::chr21:34915147..34915178,- p3@GART
Hg19::chr21:34915181..34915204,- p4@GART
Hg19::chr5:34839260..34839339,+ p1@TTC23L


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0004644phosphoribosylglycinamide formyltransferase activity0.0027375485694101
GO:0004641phosphoribosylformylglycinamidine cyclo-ligase activity0.0027375485694101
GO:0004637phosphoribosylamine-glycine ligase activity0.00456231233278836
GO:0046040IMP metabolic process0.00456231233278836
GO:0006189'de novo' IMP biosynthetic process0.00456231233278836
GO:0006188IMP biosynthetic process0.00456231233278836
GO:0009113purine base biosynthetic process0.00547461362960894
GO:0016882cyclo-ligase activity0.00602172041914822
GO:0006144purine base metabolic process0.00602172041914822
GO:0016742hydroxymethyl-, formyl- and related transferase activity0.00602172041914822
GO:0046112nucleobase biosynthetic process0.00696697213612794
GO:0009112nucleobase metabolic process0.00855181734683608
GO:0009168purine ribonucleoside monophosphate biosynthetic process0.00855181734683608
GO:0009167purine ribonucleoside monophosphate metabolic process0.00855181734683608
GO:0009127purine nucleoside monophosphate biosynthetic process0.00855181734683608
GO:0009126purine nucleoside monophosphate metabolic process0.00855181734683608
GO:0004372glycine hydroxymethyltransferase activity0.00901422339566733
GO:0009161ribonucleoside monophosphate metabolic process0.00945183586136322
GO:0009156ribonucleoside monophosphate biosynthetic process0.00945183586136322
GO:0046148pigment biosynthetic process0.00945183586136322
GO:0009124nucleoside monophosphate biosynthetic process0.00945183586136322
GO:0009123nucleoside monophosphate metabolic process0.00945183586136322
GO:0042440pigment metabolic process0.00999197011681788
GO:0019748secondary metabolic process0.0120815856858232
GO:0005524ATP binding0.0245517609060341
GO:0032559adenyl ribonucleotide binding0.0245517609060341
GO:0030554adenyl nucleotide binding0.0253718292786105
GO:0046483heterocycle metabolic process0.0253718292786105
GO:0009152purine ribonucleotide biosynthetic process0.0262962846519019
GO:0009150purine ribonucleotide metabolic process0.0262962846519019
GO:0009260ribonucleotide biosynthetic process0.0262962846519019
GO:0016740transferase activity0.0262962846519019
GO:0006164purine nucleotide biosynthetic process0.0262962846519019
GO:0006163purine nucleotide metabolic process0.0262962846519019
GO:0009259ribonucleotide metabolic process0.0262962846519019
GO:0032553ribonucleotide binding0.0262962846519019
GO:0032555purine ribonucleotide binding0.0262962846519019
GO:0006725aromatic compound metabolic process0.0262962846519019
GO:0017076purine nucleotide binding0.0273848872620982
GO:0009165nucleotide biosynthetic process0.0347732572115841
GO:0000166nucleotide binding0.0351870221378261
GO:0008168methyltransferase activity0.0351870221378261
GO:0016741transferase activity, transferring one-carbon groups0.0352528252605742
GO:0009117nucleotide metabolic process0.042096473073867
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.0439173729042794
GO:0016879ligase activity, forming carbon-nitrogen bonds0.0439173729042794



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
classical monocyte2.64e-3542
CD14-positive, CD16-negative classical monocyte2.64e-3542
leukocyte2.73e-31136
defensive cell1.54e-2848
phagocyte1.54e-2848
myeloid leukocyte4.87e-2872
hematopoietic lineage restricted progenitor cell6.37e-27120
nongranular leukocyte4.78e-24115
myeloid lineage restricted progenitor cell7.23e-2466
granulocyte monocyte progenitor cell9.83e-2467
macrophage dendritic cell progenitor1.94e-2261
hematopoietic stem cell3.70e-22168
angioblastic mesenchymal cell3.70e-22168
monopoietic cell5.31e-2159
monocyte5.31e-2159
monoblast5.31e-2159
promonocyte5.31e-2159
hematopoietic cell7.31e-21177
hematopoietic oligopotent progenitor cell1.59e-19161
hematopoietic multipotent progenitor cell1.59e-19161
myeloid cell1.66e-15108
common myeloid progenitor1.66e-15108
stuff accumulating cell1.15e-1287
intermediate monocyte1.90e-089
CD14-positive, CD16-positive monocyte1.90e-089
Uber Anatomy
Ontology termp-valuen
bone marrow7.33e-2176
hematopoietic system4.42e-2098
blood island4.42e-2098
bone element1.09e-1982
skeletal element1.38e-1790
immune system1.31e-1693
hemolymphoid system3.30e-16108
skeletal system1.26e-14100
neural tube8.88e-1256
neural rod8.88e-1256
future spinal cord8.88e-1256
neural keel8.88e-1256
regional part of nervous system3.40e-1153
regional part of brain3.40e-1153
regional part of forebrain1.73e-0941
forebrain1.73e-0941
anterior neural tube1.73e-0941
future forebrain1.73e-0941
brain grey matter1.30e-0834
gray matter1.30e-0834
central nervous system1.72e-0881
neocortex1.73e-0820
brain2.83e-0868
future brain2.83e-0868
telencephalon3.72e-0834
regional part of telencephalon1.41e-0732
cerebral hemisphere1.76e-0732
nervous system2.49e-0789
regional part of cerebral cortex2.75e-0722


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.481059
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.161847
MA0017.11.24112
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.11.7452
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.12.35759
MA0061.12.2047
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0140295
MA0074.10.730989
MA0076.11.33654
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.818263
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.12.02769
MA0103.10.442769
MA0105.11.58771
MA0106.10.779931
MA0107.12.62998
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.938075
MA0145.10.143698
MA0146.10.143081
MA0147.10.386018
MA0148.11.57313
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.20.30855
MA0137.21.20193
MA0104.20.320919
MA0047.21.80892
MA0112.20.136971
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.0442129
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CHD2#110636.206413700470110.007774550126275590.0319545942793426
E2F1#186943.925911371903460.007214984547106360.0298769188816955
E2F4#187437.600836189170660.004354147360375710.020649477621028
E2F6#187644.013724585357910.006632118233933880.0282945995193554
ELF1#199743.406478367046030.01235066105299550.044733507532991
EP300#203345.419153380978560.00209386927943890.0121166674243861
FOXA1#316936.648851849631270.006389025166568720.0278084350644413
GTF2B#2959212.77753197372970.00919936089559720.0347878938581822
HNF4G#3174211.50136901057870.01127438304921050.0413791569889125
IRF1#365946.109731002851120.001315525264767990.0088100123839118
IRF3#3661218.79278088459580.004339629777121510.0205890425790575
JUND#372745.595731153496820.001849593301755460.0109339262377335
MAFK#7975210.8402932551320.01263683277337880.0456876165063492
MXI1#460135.976942977255580.008653004889366880.0329520939887179
NANOG#79923211.69791139240510.01091164951956080.040224551345643
NFKB1#479055.488063424193840.0002008162847462320.00239063626611327
POU2F2#545235.463674434645510.01115650094469780.0410128054263741
RFX5#599349.638328661756080.000221480125815720.00249661768592207
SIN3A#2594255.408884726815140.0002159522671657270.00248062459640578
SP1#666744.558705102512720.00407573565781680.0194848373325427
SP2#6668315.69211829630680.0005272235913302770.0045634596929341
ZNF143#770238.100525931336740.003624870512090980.018331292437162



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.