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Coexpression cluster:C214: Difference between revisions

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|tf_chipseq_enrich=CTBP2#1488;7:6.36259423732314:0.000118437880671144:0.0016085219531097!NANOG#79923;8:3.39069895432031:0.00243215604043235:0.0136985355501652!RAD21#5885;20:3.00145910013227:5.22739825425055e-06:0.000160100951987001!TRIM28#10155;9:2.42485109286033:0.0114680501306614:0.0419484340009858!ZNF263#10127;22:2.62145675382949:1.35558385273272e-05:0.000328482185604531
|tf_chipseq_enrich=CTBP2#1488;7:6.36259423732314:0.000118437880671144:0.0016085219531097!NANOG#79923;8:3.39069895432031:0.00243215604043235:0.0136985355501652!RAD21#5885;20:3.00145910013227:5.22739825425055e-06:0.000160100951987001!TRIM28#10155;9:2.42485109286033:0.0114680501306614:0.0419484340009858!ZNF263#10127;22:2.62145675382949:1.35558385273272e-05:0.000328482185604531
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|tfbs_overrepresentation_for_novel_motifs=1.79292,0.169487,1.07083,0.173784,0.411791,0.571034,0.271533,0.939888,0.103225,0.538597,1.05376,0.610742,0.321899,0.255056,0.146817,0.0382658,0.326987,1.23237,0.0606791,0.218572,0.370542,0.0366663,0.548587,0.026622,0.31716,1.47227,0.0979285,0.160551,0.422255,0.178733,0.117007,0.116374,0.749484,0.608001,0.185073,1.34571,1.69009,0.864119,0.356386,0.315528,0.0989518,0.217926,0.322909,0.144495,1.52373,0.283889,0.273119,0.703557,0.196718,0.845468,0.399246,0.290541,0.253102,0.47311,0.697813,0.259213,0.279343,0.412452,0.0386816,0.21332,1.96161,0.513454,0.72016,0.613815,0.880742,0.256493,0.312137,0.611811,0.111429,0.473124,1.84716,0.298641,2.73357,0.248809,2.48083,0.47816,0.0804971,0.579917,0.109903,0.165291,0.717318,0.293427,0.302921,0.112171,1.80939,0.353605,0.211776,2.08838,1.18506,0.700455,0.382593,0.198363,0.124597,0.429552,1.39277,0.0281721,1.29633,0.146642,0.0563488,0.177635,0.713434,0.386131,0.441912,0.100972,0.523315,1.0321,0.312614,0.250209,1.7226,0.532013,0.0551035,0.862168,0.354944,2.33487,0.345782,0.437328,2.31069,0.659374,0.540972,1.04768,2.74399,0.199407,0.563016,0.918278,0.432294,0.98125,0.78774,0.399782,0.272261,1.13862,0.198787,0.963892,0.282312,0.134025,0.392663,0.299849,0.23476,0.543999,0.35979,1.12806,0.748112,0.331642,0.109,0.444663,0.246099,0.203775,2.35851,0.975366,0.21263,0.281179,0.132703,0.825815,0.199021,0.155013,3.78986,0.498621,0.416337,0.0234203,0.0257508,0.255007,0.330738,0.187783,0.109535,0.429345,0.0761307,0.553624,2.34363,0.111326,0.0774473
}}
}}

Revision as of 13:48, 26 November 2012


Full id: C214_Neurons_Neural_duodenum_temporal_occipital_parietal_brain



Phase1 CAGE Peaks

Hg19::chr10:112836138..112836159,+p@chr10:112836138..112836159
+
Hg19::chr11:57335750..57335798,-p2@UBE2L6
Hg19::chr12:111471526..111471541,+p1@CUX2
Hg19::chr12:124265636..124265639,+p3@DNAH10
Hg19::chr13:112721131..112721138,+p@chr13:112721131..112721138
+
Hg19::chr14:23956535..23956550,-p@chr14:23956535..23956550
-
Hg19::chr14:29235961..29236008,+p1@FOXG1
Hg19::chr14:29236269..29236285,+p3@FOXG1
Hg19::chr14:29236301..29236317,+p5@FOXG1
Hg19::chr17:37764128..37764258,-p1@NEUROD2
Hg19::chr17:79008476..79008509,-p2@FLJ90757
Hg19::chr18:53069389..53069416,-p40@TCF4
Hg19::chr18:53069419..53069450,-p34@TCF4
Hg19::chr1:11539204..11539219,+p1@PTCHD2
Hg19::chr1:151032922..151032951,+p2@MLLT11
Hg19::chr1:151032957..151032968,+p7@MLLT11
Hg19::chr20:656437..656451,-p4@SRXN1
Hg19::chr20:657349..657358,-p@chr20:657349..657358
-
Hg19::chr22:28197594..28197605,-p8@MN1
Hg19::chr22:42393540..42393558,+p@chr22:42393540..42393558
+
Hg19::chr22:45404770..45404812,-p2@PHF21B
Hg19::chr22:45404819..45404830,-p5@PHF21B
Hg19::chr2:104496537..104496544,-p3@ENST00000455716
Hg19::chr2:104496562..104496570,-p2@ENST00000455716
Hg19::chr2:104496621..104496635,-p1@ENST00000455716
Hg19::chr2:105050903..105050923,+p1@ENST00000447380
Hg19::chr2:105122941..105122944,+p@chr2:105122941..105122944
+
Hg19::chr2:105470536..105470556,+p4@POU3F3
Hg19::chr2:105470614..105470625,+p7@POU3F3
Hg19::chr2:5835715..5835720,+p@chr2:5835715..5835720
+
Hg19::chr2:5839854..5839869,+p@chr2:5839854..5839869
+
Hg19::chr2:85413434..85413436,+p1@TCF7L1-IT1
Hg19::chr3:115342138..115342157,+p4@GAP43
Hg19::chr3:115342159..115342173,+p5@GAP43
Hg19::chr3:36805787..36805798,-p@chr3:36805787..36805798
-
Hg19::chr3:77087811..77087819,+p@chr3:77087811..77087819
+
Hg19::chr3:89156763..89156797,+p1@EPHA3
Hg19::chr3:89156799..89156831,+p3@EPHA3
Hg19::chr3:89156832..89156848,+p2@EPHA3
Hg19::chr3:89156872..89156883,+p4@EPHA3
Hg19::chr3:89156891..89156894,+p5@EPHA3
Hg19::chr5:140613949..140613969,+p3@PCDHB18
Hg19::chr5:146257992..146258003,-p18@PPP2R2B
Hg19::chr5:150284420..150284443,-p2@ZNF300
Hg19::chr5:58295564..58295588,-p59@PDE4D
Hg19::chr5:71479302..71479315,+p@chr5:71479302..71479315
+
Hg19::chr5:87967371..87967404,-p@chr5:87967371..87967404
-
Hg19::chr6:13925142..13925163,+p3@RNF182
Hg19::chr6:13925170..13925234,+p1@RNF182
Hg19::chr6:155334892..155334903,+p18@TIAM2
Hg19::chr6:21594206..21594221,+p15@SOX4
Hg19::chr6:21594252..21594285,+p11@SOX4
Hg19::chr6:88876117..88876157,+p@chr6:88876117..88876157
+
Hg19::chr6:88877062..88877073,-p3@BC037581
Hg19::chr7:133261209..133261224,+p7@EXOC4
Hg19::chr7:133261274..133261284,+p10@EXOC4
Hg19::chr7:24323800..24323815,+p1@NPY
Hg19::chr7:24324837..24324863,+p2@NPY
Hg19::chr7:31380440..31380451,-p4@NEUROD6
Hg19::chr7:80548757..80548764,-p14@SEMA3C
Hg19::chr7:80632805..80632821,-p@chr7:80632805..80632821
-
Hg19::chr8:134114832..134114863,-p9@SLA
Hg19::chr8:134114866..134114880,-p11@SLA
Hg19::chr8:134114887..134114896,-p15@SLA
Hg19::chr8:134115035..134115072,-p12@SLA
Hg19::chr8:134115118..134115121,-p13@SLA
Hg19::chr9:14308004..14308041,-p14@NFIB
Hg19::chr9:34990264..34990312,+p3@DNAJB5
Hg19::chr9:38424443..38424458,-p1@IGFBPL1


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:0050789regulation of biological process0.0220708125053184
GO:0065007biological regulation0.0497479221438013



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
neuronal stem cell1.04e-128
neural cell2.51e-1225
astrocyte of the cerebral cortex1.15e-113
oligodendrocyte2.19e-087
macroglial cell2.19e-087
astrocyte2.19e-087
oligodendrocyte precursor cell2.19e-087
Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.33e-8053
regional part of brain1.33e-8053
central nervous system3.02e-7881
neural tube6.76e-7656
neural rod6.76e-7656
future spinal cord6.76e-7656
neural keel6.76e-7656
nervous system1.29e-6989
brain6.35e-6868
future brain6.35e-6868
telencephalon6.51e-6734
brain grey matter1.04e-6634
gray matter1.04e-6634
cerebral hemisphere6.01e-6632
regional part of forebrain1.49e-6341
forebrain1.49e-6341
anterior neural tube1.49e-6341
future forebrain1.49e-6341
regional part of telencephalon1.40e-6032
neurectoderm1.72e-5586
neural plate2.29e-5582
presumptive neural plate2.29e-5582
cerebral cortex6.12e-5425
pallium6.12e-5425
pre-chordal neural plate5.75e-4761
ecto-epithelium1.86e-44104
regional part of cerebral cortex2.33e-4422
neocortex3.55e-4320
ectoderm-derived structure1.76e-39171
ectoderm1.76e-39171
presumptive ectoderm1.76e-39171
structure with developmental contribution from neural crest3.68e-33132
adult organism2.84e-25114
organ system subdivision3.98e-25223
segmental subdivision of hindbrain2.00e-1712
hindbrain2.00e-1712
presumptive hindbrain2.00e-1712
tube2.88e-16192
segmental subdivision of nervous system5.48e-1613
gyrus2.79e-156
brainstem2.00e-146
neural nucleus3.53e-149
nucleus of brain3.53e-149
posterior neural tube1.09e-1315
chordal neural plate1.09e-1315
temporal lobe1.11e-136
regional part of metencephalon1.45e-139
metencephalon1.45e-139
future metencephalon1.45e-139
anatomical cluster1.85e-13373
occipital lobe1.02e-125
parietal lobe1.19e-125
organ part2.59e-12218
anatomical conduit2.38e-11240
pons3.19e-113
basal ganglion2.21e-109
nuclear complex of neuraxis2.21e-109
aggregate regional part of brain2.21e-109
collection of basal ganglia2.21e-109
cerebral subcortex2.21e-109
epithelium3.20e-09306
corpus striatum3.31e-094
striatum3.31e-094
ventral part of telencephalon3.31e-094
future corpus striatum3.31e-094
cell layer4.77e-09309
telencephalic nucleus8.79e-097
multi-tissue structure1.16e-08342
middle temporal gyrus2.17e-082
locus ceruleus5.63e-082
brainstem nucleus5.63e-082
hindbrain nucleus5.63e-082
limbic system1.11e-075
embryo2.08e-07592


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
CTBP2#148876.362594237323140.0001184378806711440.0016085219531097
NANOG#7992383.390698954320310.002432156040432350.0136985355501652
RAD21#5885203.001459100132275.22739825425055e-060.000160100951987001
TRIM28#1015592.424851092860330.01146805013066140.0419484340009858
ZNF263#10127222.621456753829491.35558385273272e-050.000328482185604531



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

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