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{{f5samples
 
{{f5samples
 
|DRA_sample_Accession=CAGE@SAMD00005390
 
|DRA_sample_Accession=CAGE@SAMD00005390
|accession_numbers=CAGE;DRX008261;DRR009133;DRZ000558;DRZ001943
+
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00005390
 +
|accession_numbers=CAGE;DRX008261;DRR009133;DRZ000558;DRZ001943;DRZ011908;DRZ013293
 +
|accession_numbers_RNASeq=sRNA-Seq;DRX037236;DRR041602;DRZ007244
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002384,UBERON:0000033,UBERON:0000479,UBERON:0001007,UBERON:0000344,UBERON:0004121,UBERON:0000064,UBERON:0004119,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0004923,UBERON:0000161,UBERON:0001444,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003729,UBERON:0010317,UBERON:0001555,UBERON:0001828,UBERON:0001004,UBERON:0000153,UBERON:0007811,UBERON:0000165,UBERON:0000166
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002384,UBERON:0000033,UBERON:0000479,UBERON:0001007,UBERON:0000344,UBERON:0004121,UBERON:0000064,UBERON:0004119,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0004923,UBERON:0000161,UBERON:0001444,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003729,UBERON:0010317,UBERON:0001555,UBERON:0001828,UBERON:0001004,UBERON:0000153,UBERON:0007811,UBERON:0000165,UBERON:0000166
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002320,CL:0002371,CL:0000255,CL:0000057,CL:0002552
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002320,CL:0002371,CL:0000255,CL:0000057,CL:0002552
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|microRNAs=
 
|microRNAs=
 
|microRNAs_nn=
 
|microRNAs_nn=
 +
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;11318
 
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10014.AGTCAA.11318
 
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10014.AGTCAA.11318
 +
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11318
 
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10014.AGTCAA.11318
 
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10014.AGTCAA.11318
 
|name=Fibroblast - Gingival, donor2
 
|name=Fibroblast - Gingival, donor2
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|profile_rnaseq=
 
|profile_rnaseq=
 
|profile_srnaseq=SRhi10014,,,
 
|profile_srnaseq=SRhi10014,,,
|refex=http://refex.dbcls.jp/genelist.php?lang=en&db=human&roku_valid=1&rk[]=&order_key=score
+
|refex=http://refex.dbcls.jp/genelist.php?lang
 
|repeat_enrich_byfamily=0,0,0,0,0,0,0,-0.0649155008401676,0,-0.0694124338180944,0.00422743820760335,0,0,0,0,0,0,0,0,0,0,0,0.0503156775564332,0,0.170034062061645,0,0.0251578387782166,0,0,0,-0.00255536702183901,0,0,-0.132956589778862,0,0,0,0,0,0,0,0,0,0,0,0,0.0157788192390232,0,0,0,0,0,0,0,0,0.0234862435102749,0,0,0,0.506642701092527,0,0.0224212358580788,0,-0.0969923612426051,0,0,0.0389021113308758,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0118966943612218,0.0340551615981899,0.148625714708146,0,0,-0.0799839738539042,0.0408118002959941,0,0.136245738543973,0,0.0503156775564332,0.0755405199878837,-0.0451964927506924,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0398721446215119,0.17357587122559,0,0,-0.0263941514171957,-0.128092870494113,0,0,0,0,0,0
 
|repeat_enrich_byfamily=0,0,0,0,0,0,0,-0.0649155008401676,0,-0.0694124338180944,0.00422743820760335,0,0,0,0,0,0,0,0,0,0,0,0.0503156775564332,0,0.170034062061645,0,0.0251578387782166,0,0,0,-0.00255536702183901,0,0,-0.132956589778862,0,0,0,0,0,0,0,0,0,0,0,0,0.0157788192390232,0,0,0,0,0,0,0,0,0.0234862435102749,0,0,0,0.506642701092527,0,0.0224212358580788,0,-0.0969923612426051,0,0,0.0389021113308758,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0118966943612218,0.0340551615981899,0.148625714708146,0,0,-0.0799839738539042,0.0408118002959941,0,0.136245738543973,0,0.0503156775564332,0.0755405199878837,-0.0451964927506924,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0398721446215119,0.17357587122559,0,0,-0.0263941514171957,-0.128092870494113,0,0,0,0,0,0
 
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Line 78: Line 82:
 
|rna_tube_id=117D4
 
|rna_tube_id=117D4
 
|rna_weight_ug=10
 
|rna_weight_ug=10
 +
|rnaseq_library_id=SRhi10014.AGTCAA
 
|sample_age=fetal
 
|sample_age=fetal
 
|sample_category=primary cells
 
|sample_category=primary cells

Latest revision as of 06:26, 17 October 2017

Name:Fibroblast - Gingival, donor2
Species:Human (Homo sapiens)
Library ID:CNhs11961
Sample type:primary cells
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samplessRNA samples)
Excluding candidate novel miRNAs(CAGE samplessRNA samples)
RefEX:Specific genes
FANTOM CAT:1, 2, 3, 4, 5, 6, 7, 8, 9, 10
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuegum
dev stagefetus
sexunknown
agefetal
cell typefibroblast
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number3540
catalog numberSC2625
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005390
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11961 CAGE DRX008261 DRR009133
Accession ID Hg19

Library idBAMCTSS
CNhs11961 DRZ000558 DRZ001943
Accession ID Hg38

Library idBAMCTSS
CNhs11961 DRZ011908 DRZ013293
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00005390
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10014.AGTCAA sRNA-Seq DRX037236 DRR041602
Accession ID Hg19

Library idBAMCTSS
SRhi10014.AGTCAA DRZ007244


Relative expression to median (log10)


Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
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C81-trachea-salivary-throat-aorta-eye-submaxillary-parotid0
C82-Basophils-CD14-Eosinophils-Natural-Peripheral-immature-CD340
C83-choriocarcinoma-pancreatic-placenta-chorionic-HES3GFP-testicular-amniotic0
C84-choriocarcinoma-pancreatic-Wilms-Mallassezderived-thymus-salivary-colon0
C85-neuroblastoma-carcinoid-retinoblastoma-small-pineal-rhabdomyosarcoma-medulloblastoma0
C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs11961

Jaspar motif P-value
MA0002.2 0.0218
MA0003.1 0.426
MA0004.1 0.506
MA0006.1 0.862
MA0007.1 0.347
MA0009.1 0.718
MA0014.1 0.276
MA0017.1 0.115
MA0018.2 3.5504e-4
MA0019.1 0.0339
MA0024.1 1.45693e-7
MA0025.1 4.84202e-5
MA0027.1 0.675
MA0028.1 0.0862
MA0029.1 0.766
MA0030.1 0.039
MA0031.1 0.0108
MA0035.2 0.0101
MA0038.1 0.106
MA0039.2 0.521
MA0040.1 0.286
MA0041.1 0.21
MA0042.1 0.427
MA0043.1 1.27182e-5
MA0046.1 0.1
MA0047.2 0.17
MA0048.1 1.85358e-5
MA0050.1 0.00522
MA0051.1 0.00637
MA0052.1 0.133
MA0055.1 5.61985e-4
MA0057.1 0.28
MA0058.1 0.181
MA0059.1 0.944
MA0060.1 6.80374e-4
MA0061.1 1.92876e-4
MA0062.2 0.102
MA0065.2 0.357
MA0066.1 0.797
MA0067.1 0.0041
MA0068.1 0.41
MA0069.1 0.399
MA0070.1 0.988
MA0071.1 0.835
MA0072.1 0.385
MA0073.1 0.283
MA0074.1 0.671
MA0076.1 0.631
MA0077.1 0.939
MA0078.1 0.954
MA0079.2 0.0826
MA0080.2 3.2403e-10
MA0081.1 0.048
MA0083.1 0.0878
MA0084.1 0.0398
MA0087.1 0.865
MA0088.1 0.00791
MA0090.1 0.323
MA0091.1 0.706
MA0092.1 0.19
MA0093.1 0.4
MA0099.2 0.0163
MA0100.1 0.144
MA0101.1 2.88886e-4
MA0102.2 0.00117
MA0103.1 0.0344
MA0104.2 0.965
MA0105.1 0.274
MA0106.1 0.327
MA0107.1 3.59626e-7
MA0108.2 0.0173
MA0111.1 0.971
MA0112.2 0.582
MA0113.1 0.917
MA0114.1 0.235
MA0115.1 0.932
MA0116.1 0.916
MA0117.1 0.164
MA0119.1 0.0754
MA0122.1 0.19
MA0124.1 0.658
MA0125.1 0.532
MA0131.1 0.472
MA0135.1 0.131
MA0136.1 4.61585e-10
MA0137.2 0.00857
MA0138.2 0.853
MA0139.1 0.628
MA0140.1 0.0659
MA0141.1 0.679
MA0142.1 0.338
MA0143.1 0.365
MA0144.1 0.0578
MA0145.1 0.122
MA0146.1 0.0798
MA0147.1 0.743
MA0148.1 0.258
MA0149.1 0.232
MA0150.1 0.00845
MA0152.1 0.0871
MA0153.1 0.077
MA0154.1 0.0904
MA0155.1 0.425
MA0156.1 3.0224e-7
MA0157.1 0.00714
MA0159.1 0.00674
MA0160.1 0.182
MA0162.1 0.0141
MA0163.1 0.106
MA0164.1 0.609
MA0258.1 0.876
MA0259.1 0.516



FANTOM5 phase1 novel unique motifsSummary:Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs11961

Novel motif P-value
1 0.891
10 0.0477
100 0.155
101 0.953
102 0.668
103 0.342
104 0.948
105 0.329
106 0.00622
107 0.958
108 0.868
109 0.38
11 0.39
110 0.0228
111 0.598
112 0.552
113 0.0435
114 0.256
115 0.0476
116 0.15
117 0.0733
118 0.456
119 0.643
12 0.597
120 0.142
121 0.728
122 0.0139
123 0.504
124 0.567
125 0.531
126 0.652
127 0.743
128 0.593
129 0.612
13 0.863
130 0.211
131 0.191
132 0.565
133 0.75
134 0.673
135 0.00563
136 0.159
137 0.0703
138 0.481
139 0.00144
14 0.188
140 0.967
141 0.332
142 0.542
143 0.219
144 0.46
145 0.247
146 0.547
147 0.184
148 0.595
149 0.747
15 0.421
150 0.601
151 0.707
152 0.312
153 0.969
154 0.431
155 0.204
156 0.213
157 0.168
158 0.0197
159 0.297
16 0.862
160 0.0666
161 0.716
162 0.098
163 0.623
164 0.219
165 0.788
166 0.667
167 0.99
168 0.363
169 0.801
17 0.601
18 0.774
19 0.239
2 0.838
20 0.431
21 3.83236e-4
22 0.723
23 0.139
24 0.972
25 0.347
26 0.0357
27 0.69
28 0.317
29 0.617
3 0.559
30 0.684
31 0.73
32 0.0698
33 0.429
34 0.275
35 0.341
36 0.41
37 0.349
38 0.563
39 0.859
4 0.0637
40 0.785
41 0.019
42 0.964
43 0.314
44 0.305
45 0.0513
46 0.779
47 0.774
48 0.337
49 0.294
5 0.0921
50 0.354
51 0.722
52 0.172
53 0.659
54 0.694
55 0.949
56 0.985
57 0.405
58 0.166
59 0.986
6 0.439
60 0.0653
61 0.733
62 0.315
63 0.537
64 0.743
65 0.423
66 0.315
67 0.374
68 0.954
69 0.48
7 0.245
70 0.162
71 0.902
72 0.225
73 0.688
74 0.237
75 0.662
76 0.284
77 0.803
78 0.696
79 0.575
8 0.196
80 0.00223
81 0.858
82 0.151
83 0.366
84 0.676
85 0.0956
86 0.147
87 0.344
88 0.206
89 0.336
9 0.408
90 0.518
91 0.673
92 0.245
93 0.292
94 0.783
95 0.213
96 0.512
97 0.633
98 0.291
99 3.25337e-4



de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: CNhs11961


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0000057 (fibroblast)
0002552 (fibroblast of gingiva)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002384 (connective tissue)
0000033 (head)
0000479 (tissue)
0001007 (digestive system)
0000344 (mucosa)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0004119 (endoderm-derived structure)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0004923 (organ component layer)
0000161 (orifice)
0001444 (subdivision of head)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003729 (mouth mucosa)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0001828 (gingiva)
0001004 (respiratory system)
0000153 (anterior region of body)
0007811 (craniocervical region)
0000165 (mouth)
0000166 (oral opening)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000057 (fibroblast sample)
0000001 (sample)
0000063 (human fibroblast of gingiva sample)

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

CL:0000134 (mesenchymal cell)