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Revision as of 19:44, 15 May 2017

Name:Fibroblast - Gingival, donor5 (GFH3)
Species:Human (Homo sapiens)
Library ID:CNhs11952
Sample type:primary cells
Genomic View: UCSC
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 stage22 years old adult
sexmale
age22
cell typefibroblast
cell lineNA
companyN/A
collaborationMitsuhiro Ohshima (Nihon University School of Dentistry)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004968
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11952 CAGE DRX008264 DRR009136
Accession ID Hg19

Library idBAMCTSS
CNhs11952 DRZ000561 DRZ001946
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]


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. <br>Analyst:NA <br><br>link to dataset.<br>data

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0.0138
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.128
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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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 sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data



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

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs11952

Jaspar motifP-value
MA0002.20.0297
MA0003.10.353
MA0004.10.305
MA0006.10.0659
MA0007.10.826
MA0009.10.68
MA0014.10.346
MA0017.10.266
MA0018.20.00139
MA0019.10.82
MA0024.10.00743
MA0025.10.00115
MA0027.10.775
MA0028.16.7767e-4
MA0029.10.585
MA0030.10.425
MA0031.10.0789
MA0035.20.00272
MA0038.10.0404
MA0039.22.15345e-4
MA0040.10.509
MA0041.10.599
MA0042.10.622
MA0043.12.1055e-4
MA0046.10.132
MA0047.20.316
MA0048.10.18
MA0050.11.75767e-4
MA0051.10.00183
MA0052.10.198
MA0055.10.346
MA0057.10.392
MA0058.10.125
MA0059.10.16
MA0060.11.93306e-10
MA0061.10.295
MA0062.27.21861e-11
MA0065.20.528
MA0066.10.81
MA0067.10.00854
MA0068.10.425
MA0069.10.196
MA0070.10.835
MA0071.10.989
MA0072.10.438
MA0073.10.72
MA0074.10.188
MA0076.16.71128e-5
MA0077.10.349
MA0078.10.618
MA0079.20.643
MA0080.21.65009e-9
MA0081.10.0047
MA0083.10.0508
MA0084.10.0964
MA0087.10.785
MA0088.10.193
MA0090.10.0292
MA0091.10.087
MA0092.10.687
MA0093.10.226
MA0099.22.88628e-5
MA0100.10.502
MA0101.10.059
MA0102.20.811
MA0103.10.0204
MA0104.20.00168
MA0105.10.234
MA0106.10.26
MA0107.10.0844
MA0108.20.714
MA0111.10.942
MA0112.20.143
MA0113.10.975
MA0114.10.241
MA0115.10.232
MA0116.10.508
MA0117.10.0837
MA0119.10.368
MA0122.10.202
MA0124.10.103
MA0125.10.517
MA0131.10.179
MA0135.10.44
MA0136.12.0319e-14
MA0137.20.267
MA0138.20.513
MA0139.10.498
MA0140.10.00458
MA0141.10.933
MA0142.10.135
MA0143.10.757
MA0144.10.82
MA0145.10.87
MA0146.10.708
MA0147.15.3792e-4
MA0148.10.506
MA0149.10.407
MA0150.10.0037
MA0152.10.0159
MA0153.10.478
MA0154.10.686
MA0155.10.143
MA0156.13.60967e-11
MA0157.10.203
MA0159.10.23
MA0160.10.304
MA0162.10.0726
MA0163.10.499
MA0164.10.814
MA0258.10.158
MA0259.10.0146



FANTOM5 phase1 novel unique motifs<b>Summary:</b>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 in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs11952

Novel motifP-value
10.266
100.814
1000.867
1010.2
1020.0831
1030.843
1040.542
1050.0837
1060.129
1070.0803
1080.317
1090.815
110.685
1100.802
1110.613
1120.783
1130.969
1140.597
1150.00118
1160.0426
1170.625
1180.607
1190.839
120.0489
1200.306
1210.979
1220.0254
1230.0552
1240.624
1250.92
1260.918
1270.843
1280.0943
1290.307
130.0557
1300.853
1310.483
1320.343
1330.213
1340.222
1350.904
1360.0808
1370.728
1380.994
1390.55
140.24
1400.638
1410.0591
1420.923
1430.816
1440.328
1450.72
1460.566
1470.283
1480.472
1490.209
150.229
1500.121
1510.788
1520.00338
1530.905
1540.512
1550.111
1560.961
1570.364
1580.0501
1590.82
160.135
1600.89
1610.874
1620.251
1630.781
1640.258
1650.905
1660.0245
1670.379
1680.562
1690.23
170.76
180.307
190.0096
20.286
200.481
210.151
220.471
230.354
240.146
250.182
260.332
270.855
280.154
290.775
30.888
300.459
310.751
321.03151e-17
330.805
340.92
350.564
360.0138
370.427
380.256
390.626
40.236
400.0442
410.493
420.218
430.968
440.379
450.992
460.59
470.405
480.422
490.267
50.59
500.555
510.929
520.578
530.0807
540.673
550.219
560.861
570.782
580.239
590.0379
60.73
600.996
610.782
620.78
630.479
640.467
650.735
660.104
670.825
680.402
690.604
70.086
700.492
710.624
720.373
730.0215
740.518
750.626
760.177
770.2
780.218
793.82121e-4
80.556
800.039
810.659
820.883
830.094
840.98
850.115
860.426
870.439
880.294
890.105
90.608
900.403
910.775
920.686
930.341
940.852
950.839
960.369
970.689
980.203
990.00422



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs11952


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>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)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
CL:0000134 (mesenchymal cell)

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