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FF:11380-118B3: 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 17:05, 29 March 2012


Name:Fibroblast - Periodontal Ligament, donor6 (PLH3)
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 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
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-0.0712
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-0.0667
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: CNhs11996

Jaspar motifP-value
MA0002.20.0357
MA0003.10.555
MA0004.10.664
MA0006.10.23
MA0007.10.82
MA0009.10.613
MA0014.10.38
MA0017.10.122
MA0018.20.351
MA0019.10.714
MA0024.10.242
MA0025.10.0825
MA0027.10.613
MA0028.10.0265
MA0029.10.074
MA0030.10.96
MA0031.10.465
MA0035.20.00665
MA0038.10.282
MA0039.20.0575
MA0040.10.191
MA0041.10.201
MA0042.10.26
MA0043.10.0899
MA0046.10.882
MA0047.20.767
MA0048.10.601
MA0050.11.21002e-5
MA0051.11.77427e-5
MA0052.10.704
MA0055.10.188
MA0057.10.64
MA0058.10.569
MA0059.10.0837
MA0060.19.27316e-4
MA0061.10.106
MA0062.22.89467e-5
MA0065.20.0184
MA0066.10.503
MA0067.10.177
MA0068.10.023
MA0069.10.504
MA0070.10.656
MA0071.10.596
MA0072.10.391
MA0073.10.881
MA0074.10.466
MA0076.10.0204
MA0077.10.677
MA0078.10.614
MA0079.20.296
MA0080.21.64927e-8
MA0081.10.0273
MA0083.10.00814
MA0084.10.269
MA0087.10.505
MA0088.10.0771
MA0090.10.00169
MA0091.10.524
MA0092.10.821
MA0093.10.67
MA0099.20.0394
MA0100.10.561
MA0101.10.387
MA0102.20.52
MA0103.10.00221
MA0104.20.00553
MA0105.11.49553e-4
MA0106.10.607
MA0107.10.391
MA0108.28.47123e-6
MA0111.10.246
MA0112.20.231
MA0113.10.804
MA0114.10.0784
MA0115.10.167
MA0116.14.07547e-4
MA0117.10.312
MA0119.10.367
MA0122.10.466
MA0124.10.701
MA0125.10.204
MA0131.10.564
MA0135.10.359
MA0136.11.6243e-10
MA0137.20.884
MA0138.20.584
MA0139.10.0714
MA0140.10.0184
MA0141.10.412
MA0142.10.138
MA0143.10.654
MA0144.10.967
MA0145.10.649
MA0146.10.715
MA0147.10.00142
MA0148.10.963
MA0149.10.336
MA0150.10.0312
MA0152.10.0641
MA0153.10.826
MA0154.10.0183
MA0155.10.575
MA0156.11.0664e-5
MA0157.10.442
MA0159.10.0537
MA0160.10.435
MA0162.10.583
MA0163.14.6956e-4
MA0164.10.673
MA0258.10.443
MA0259.10.0492



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: CNhs11996

Novel motifP-value
10.0215
100.169
1000.436
1010.168
1020.132
1030.382
1040.48
1050.153
1060.988
1070.528
1080.721
1090.348
110.147
1100.0619
1110.14
1120.656
1130.183
1140.0621
1150.0249
1160.597
1170.0784
1180.0575
1190.0715
120.26
1200.805
1210.327
1220.237
1230.00189
1240.209
1250.859
1260.465
1270.732
1280.483
1290.161
130.0431
1300.22
1310.751
1320.398
1330.259
1340.0514
1350.975
1360.17
1370.993
1380.487
1390.011
140.361
1400.196
1410.00279
1420.997
1430.734
1440.487
1450.431
1460.657
1470.287
1480.306
1490.806
150.134
1500.527
1510.635
1520.0176
1530.352
1540.94
1550.0272
1560.641
1570.0919
1580.0135
1590.434
160.684
1600.211
1610.419
1620.792
1630.76
1640.708
1650.643
1660.0228
1670.206
1680.375
1690.531
170.662
180.952
190.53
20.563
200.505
210.98
220.864
230.856
240.197
250.139
260.755
270.719
280.297
290.163
30.177
300.302
310.93
321.20706e-8
330.637
340.889
350.121
360.00886
370.468
380.232
390.805
40.288
400.0477
410.335
420.0967
430.37
440.666
450.875
460.267
470.032
480.0834
490.0965
50.421
500.62
510.655
520.639
530.15
540.867
550.878
560.428
570.185
580.199
590.518
60.948
600.643
610.399
620.233
630.865
640.177
650.894
660.365
670.987
680.22
690.933
70.0582
700.301
710.052
720.339
730.33
740.814
750.0711
760.911
770.993
780.0365
790.00651
80.456
800.292
810.312
820.0801
830.372
840.907
850.366
860.742
870.184
880.578
890.654
90.732
900.0663
910.218
920.505
930.394
940.223
950.531
960.214
970.468
980.145
990.06



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: CNhs11996


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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