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FF:11395-118C9: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 17:00, 29 March 2012


Name:Fibroblast - Periodontal Ligament, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueperiodontal ligament
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 number437
catalog numberSC2635
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
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-penis-0.177
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-lymphoma0.458
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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 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 no result for this sample


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: CNhs11907

Jaspar motifP-value
MA0002.20.855
MA0003.10.693
MA0004.10.688
MA0006.10.879
MA0007.10.555
MA0009.10.357
MA0014.10.0941
MA0017.10.464
MA0018.20.047
MA0019.10.695
MA0024.10.00678
MA0025.10.227
MA0027.10.477
MA0028.10.0342
MA0029.10.108
MA0030.10.198
MA0031.10.153
MA0035.20.212
MA0038.10.00225
MA0039.20.0407
MA0040.10.171
MA0041.10.332
MA0042.10.292
MA0043.10.0537
MA0046.10.312
MA0047.20.0298
MA0048.10.676
MA0050.10.239
MA0051.10.995
MA0052.10.892
MA0055.10.436
MA0057.10.809
MA0058.10.603
MA0059.10.323
MA0060.16.42919e-6
MA0061.10.00461
MA0062.20.174
MA0065.20.0138
MA0066.10.245
MA0067.10.288
MA0068.10.253
MA0069.10.584
MA0070.10.726
MA0071.10.189
MA0072.10.673
MA0073.10.722
MA0074.10.347
MA0076.10.0288
MA0077.10.181
MA0078.10.499
MA0079.20.585
MA0080.20.0361
MA0081.10.705
MA0083.10.113
MA0084.10.185
MA0087.10.402
MA0088.10.0921
MA0090.10.0186
MA0091.10.996
MA0092.10.976
MA0093.10.718
MA0099.22.46697e-11
MA0100.10.0296
MA0101.10.301
MA0102.20.419
MA0103.12.24755e-5
MA0104.20.696
MA0105.16.26572e-5
MA0106.10.632
MA0107.10.0736
MA0108.20.622
MA0111.10.259
MA0112.20.0231
MA0113.10.41
MA0114.10.365
MA0115.10.326
MA0116.10.00213
MA0117.10.673
MA0119.10.815
MA0122.10.662
MA0124.10.0811
MA0125.10.738
MA0131.10.577
MA0135.10.242
MA0136.10.873
MA0137.20.0365
MA0138.20.194
MA0139.10.506
MA0140.10.383
MA0141.10.165
MA0142.10.497
MA0143.10.269
MA0144.10.228
MA0145.10.841
MA0146.10.419
MA0147.10.717
MA0148.10.146
MA0149.10.768
MA0150.10.114
MA0152.10.453
MA0153.10.837
MA0154.10.0318
MA0155.10.127
MA0156.10.528
MA0157.10.349
MA0159.10.00386
MA0160.10.492
MA0162.10.847
MA0163.18.40149e-4
MA0164.10.377
MA0258.10.0193
MA0259.10.716



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: CNhs11907

Novel motifP-value
10.0706
100.6
1000.302
1010.677
1020.196
1030.685
1040.438
1050.763
1060.0217
1070.447
1080.304
1090.894
110.269
1100.531
1110.326
1120.119
1130.0103
1140.497
1150.311
1160.288
1170.436
1180.298
1190.0292
120.661
1200.683
1210.441
1220.938
1239.76366e-5
1240.748
1250.33
1260.495
1270.668
1280.295
1290.979
130.135
1300.01
1310.941
1320.28
1330.86
1340.0785
1350.296
1360.88
1370.893
1380.387
1391.14668e-4
140.267
1400.347
1410.598
1420.914
1430.769
1440.799
1450.958
1460.307
1470.136
1480.786
1490.629
150.606
1500.61
1510.18
1520.96
1530.66
1540.85
1550.0279
1560.888
1570.312
1580.0487
1590.23
160.505
1600.0687
1610.5
1620.324
1630.321
1640.143
1650.249
1660.617
1670.345
1680.838
1690.284
170.335
180.879
190.786
20.641
200.596
210.638
220.866
230.547
240.166
250.287
260.654
270.746
280.695
290.224
30.257
300.313
310.544
320.178
330.863
340.469
350.0249
360.1
370.38
380.651
390.523
40.339
400.0409
410.909
420.98
430.419
440.0167
450.795
460.173
470.111
480.315
490.307
50.585
500.406
510.859
520.714
530.321
540.873
550.309
560.583
570.949
580.116
590.363
60.847
600.0778
610.701
620.0576
630.539
640.129
650.145
660.0276
670.632
680.392
690.546
70.255
700.0109
710.291
720.891
730.72
740.158
750.16
760.643
770.668
780.379
790.325
80.229
800.579
810.196
820.00382
830.986
840.693
850.0155
860.381
870.256
880.854
890.377
90.637
900.599
910.686
920.716
930.942
940.402
950.479
960.58
970.2
980.367
990.0539



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: CNhs11907


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)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000057 (fibroblast)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002556 (fibroblast of periodontium)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0001758 (periodontium)
0002384 (connective tissue)
0003672 (dentition)

FF: FANTOM5
NA

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
NA

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