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FF:11304-117B8: 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 17:02, 29 March 2012


Name:Fibroblast - Periodontal Ligament, donor5 (PL30)
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 stage40 years old adult
sexmale
age40
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
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-0.0356
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-lymphoma0.0562
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs11953

Jaspar motifP-value
MA0002.20.956
MA0003.10.332
MA0004.10.341
MA0006.10.0689
MA0007.10.509
MA0009.10.615
MA0014.10.845
MA0017.10.992
MA0018.21.20193e-5
MA0019.10.97
MA0024.10.0174
MA0025.10.00109
MA0027.10.97
MA0028.10.251
MA0029.10.419
MA0030.10.00269
MA0031.10.00306
MA0035.20.00574
MA0038.10.206
MA0039.20.0116
MA0040.10.267
MA0041.10.78
MA0042.10.615
MA0043.11.64904e-4
MA0046.10.263
MA0047.20.125
MA0048.10.0352
MA0050.10.239
MA0051.10.599
MA0052.10.694
MA0055.10.964
MA0057.10.122
MA0058.10.123
MA0059.10.962
MA0060.11.40203e-5
MA0061.10.475
MA0062.21.07904e-4
MA0065.20.73
MA0066.10.117
MA0067.10.0103
MA0068.10.533
MA0069.10.0258
MA0070.10.83
MA0071.10.458
MA0072.10.623
MA0073.10.966
MA0074.10.238
MA0076.10.0722
MA0077.10.444
MA0078.10.607
MA0079.20.798
MA0080.21.5529e-8
MA0081.10.0164
MA0083.17.77384e-4
MA0084.10.0612
MA0087.10.696
MA0088.10.475
MA0090.10.00443
MA0091.10.0502
MA0092.10.0996
MA0093.10.228
MA0099.20.25
MA0100.10.911
MA0101.10.00527
MA0102.20.0153
MA0103.10.0602
MA0104.20.0355
MA0105.10.516
MA0106.10.0188
MA0107.10.00679
MA0108.20.655
MA0111.10.652
MA0112.22.15874e-4
MA0113.10.535
MA0114.10.561
MA0115.10.327
MA0116.10.0724
MA0117.10.528
MA0119.10.0314
MA0122.10.152
MA0124.10.258
MA0125.10.119
MA0131.10.273
MA0135.10.611
MA0136.11.50477e-10
MA0137.20.0452
MA0138.20.418
MA0139.10.755
MA0140.10.0572
MA0141.10.29
MA0142.10.748
MA0143.10.593
MA0144.10.95
MA0145.10.27
MA0146.10.442
MA0147.10.0508
MA0148.10.341
MA0149.10.109
MA0150.10.308
MA0152.10.159
MA0153.10.416
MA0154.10.201
MA0155.10.296
MA0156.13.9062e-7
MA0157.10.15
MA0159.10.902
MA0160.10.404
MA0162.10.0449
MA0163.10.00137
MA0164.10.643
MA0258.10.0181
MA0259.10.0836



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: CNhs11953

Novel motifP-value
10.434
100.179
1000.793
1010.397
1020.199
1030.451
1040.462
1050.328
1060.0157
1070.0302
1080.288
1090.187
110.231
1100.433
1110.816
1120.141
1130.0168
1140.301
1150.0214
1160.0205
1170.613
1180.721
1190.624
120.161
1200.192
1210.619
1220.049
1230.135
1240.674
1250.135
1260.935
1270.827
1280.0372
1290.87
130.923
1300.86
1310.813
1320.537
1330.549
1340.169
1350.648
1360.265
1370.319
1380.624
1390.909
140.531
1400.425
1410.269
1420.842
1430.642
1440.74
1450.399
1460.906
1470.125
1480.983
1490.047
150.714
1500.153
1510.634
1520.00347
1530.987
1540.331
1550.0188
1560.884
1570.153
1580.00363
1590.317
160.019
1600.261
1610.729
1620.645
1630.978
1640.217
1650.314
1660.0345
1670.744
1680.966
1690.0409
170.232
180.128
190.00416
20.316
200.545
210.0719
220.21
230.576
240.987
250.793
260.13
270.686
280.283
290.491
30.296
300.633
310.602
321.19574e-16
330.239
340.801
350.994
360.0645
370.0332
380.677
390.373
40.713
400.893
410.862
420.914
430.293
440.112
450.994
460.123
470.524
480.568
490.638
50.714
500.633
510.735
520.357
530.556
540.512
550.0695
560.984
570.553
580.737
590.00464
60.36
600.366
610.842
620.475
630.166
640.856
650.263
660.838
670.627
680.983
690.222
70.488
700.14
710.0959
720.372
730.00354
740.284
750.414
760.564
770.0109
780.645
790.0016
80.0322
800.162
810.959
820.208
830.293
840.76
850.0291
860.295
870.0212
880.261
890.0175
90.699
900.631
910.88
920.33
930.539
940.676
950.187
960.748
970.901
980.445
990.00644



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: CNhs11953


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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