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FF:11319-117D5: 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 17:03, 29 March 2012


Name:Fibroblast - Periodontal Ligament, donor2
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 number1847
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-0.0438
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-lymphoma0.638
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: CNhs11962

Jaspar motifP-value
MA0002.20.00463
MA0003.10.0837
MA0004.10.351
MA0006.10.951
MA0007.10.989
MA0009.10.373
MA0014.10.621
MA0017.10.0136
MA0018.20.0804
MA0019.10.251
MA0024.12.45503e-10
MA0025.10.0158
MA0027.10.647
MA0028.10.184
MA0029.10.416
MA0030.10.431
MA0031.10.148
MA0035.20.0134
MA0038.12.69393e-4
MA0039.20.95
MA0040.10.521
MA0041.10.24
MA0042.10.541
MA0043.10.00978
MA0046.10.891
MA0047.20.534
MA0048.16.31088e-4
MA0050.12.72588e-5
MA0051.13.95241e-4
MA0052.10.626
MA0055.10.0107
MA0057.10.906
MA0058.10.147
MA0059.10.259
MA0060.18.12898e-13
MA0061.12.21921e-4
MA0062.20.39
MA0065.20.0116
MA0066.10.623
MA0067.10.0229
MA0068.10.138
MA0069.10.267
MA0070.10.197
MA0071.10.738
MA0072.10.737
MA0073.10.493
MA0074.10.77
MA0076.10.253
MA0077.10.526
MA0078.10.867
MA0079.20.723
MA0080.21.36476e-12
MA0081.10.0812
MA0083.10.24
MA0084.10.0465
MA0087.10.984
MA0088.10.0533
MA0090.10.589
MA0091.10.427
MA0092.10.111
MA0093.10.34
MA0099.20.102
MA0100.10.0706
MA0101.10.0114
MA0102.20.00747
MA0103.17.40948e-4
MA0104.20.567
MA0105.16.66588e-5
MA0106.10.875
MA0107.12.92615e-4
MA0108.20.163
MA0111.10.732
MA0112.20.00103
MA0113.10.71
MA0114.10.0571
MA0115.10.905
MA0116.10.00808
MA0117.10.445
MA0119.10.957
MA0122.10.377
MA0124.10.435
MA0125.10.37
MA0131.10.363
MA0135.10.358
MA0136.13.20723e-11
MA0137.20.21
MA0138.20.382
MA0139.10.156
MA0140.10.247
MA0141.10.501
MA0142.10.42
MA0143.10.301
MA0144.10.103
MA0145.10.114
MA0146.10.987
MA0147.10.662
MA0148.10.243
MA0149.10.899
MA0150.10.0137
MA0152.10.0316
MA0153.10.143
MA0154.10.0019
MA0155.10.187
MA0156.18.10281e-5
MA0157.10.113
MA0159.16.86847e-4
MA0160.10.148
MA0162.10.837
MA0163.10.042
MA0164.10.605
MA0258.10.0173
MA0259.10.814



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: CNhs11962

Novel motifP-value
10.263
100.988
1000.839
1010.542
1020.936
1030.0786
1040.843
1050.464
1060.00116
1070.286
1080.481
1090.373
110.454
1100.577
1110.683
1120.0446
1130.102
1140.0407
1150.707
1160.791
1170.814
1180.643
1190.2
120.968
1200.3
1210.832
1220.0603
1230.0525
1240.425
1250.771
1260.695
1270.519
1280.106
1290.208
130.486
1300.0135
1310.226
1320.883
1330.313
1340.306
1350.00135
1360.464
1370.199
1380.116
1395.99888e-5
140.163
1400.943
1410.535
1420.963
1430.0717
1440.666
1450.936
1460.881
1470.72
1480.114
1490.254
150.181
1500.784
1510.179
1520.0471
1530.877
1540.979
1550.188
1560.589
1570.101
1580.0204
1590.188
160.615
1600.744
1610.571
1620.206
1630.802
1640.593
1650.275
1660.993
1670.26
1680.287
1690.0421
170.22
180.567
190.992
20.66
200.578
210.298
220.597
230.0545
240.954
250.336
260.756
270.247
280.476
290.57
30.355
300.933
310.497
320.96
330.921
340.444
350.245
360.0882
370.132
380.402
390.794
40.457
400.172
410.0452
420.732
430.22
440.38
450.274
460.382
470.43
480.59
490.19
50.1
500.546
510.552
520.184
530.361
540.728
550.934
560.888
570.785
580.0491
590.471
60.932
600.00905
610.678
620.0486
630.735
640.514
650.13
660.0884
670.519
680.54
690.478
70.155
700.0308
710.233
720.249
730.11
740.957
750.244
760.766
770.329
780.631
790.842
80.512
800.00708
810.415
820.00592
830.381
840.937
850.00226
860.285
870.339
880.461
890.0601
90.461
900.279
910.866
920.105
930.752
940.311
950.347
960.284
970.966
980.102
990.0264



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: CNhs11962


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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