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FF:11223-116B8: 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 17:20, 29 March 2012


Name:Fibroblast - Periodontal Ligament, donor4 (PL29)
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 stage18 years old adult
sexfemale
age18
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-0.124
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-lymphoma0.227
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
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs12493

Jaspar motifP-value
MA0002.20.967
MA0003.10.968
MA0004.10.0331
MA0006.10.0547
MA0007.10.431
MA0009.10.195
MA0014.10.64
MA0017.10.173
MA0018.22.67893e-4
MA0019.10.794
MA0024.10.508
MA0025.10.0649
MA0027.10.584
MA0028.10.0033
MA0029.10.107
MA0030.10.255
MA0031.10.0703
MA0035.20.0888
MA0038.10.0925
MA0039.20.0245
MA0040.10.082
MA0041.10.156
MA0042.10.19
MA0043.11.58002e-5
MA0046.10.604
MA0047.20.338
MA0048.10.206
MA0050.10.234
MA0051.10.856
MA0052.10.137
MA0055.10.805
MA0057.10.281
MA0058.10.00688
MA0059.10.0185
MA0060.10.174
MA0061.10.0454
MA0062.29.91866e-7
MA0065.20.0417
MA0066.10.971
MA0067.10.0252
MA0068.10.571
MA0069.10.27
MA0070.10.202
MA0071.10.733
MA0072.10.683
MA0073.10.708
MA0074.10.898
MA0076.10.0059
MA0077.10.91
MA0078.10.908
MA0079.20.939
MA0080.25.73563e-10
MA0081.10.0154
MA0083.12.07433e-4
MA0084.10.0233
MA0087.10.332
MA0088.10.464
MA0090.19.25736e-6
MA0091.10.2
MA0092.10.617
MA0093.10.0638
MA0099.20.179
MA0100.10.641
MA0101.10.00428
MA0102.20.00646
MA0103.13.2739e-5
MA0104.28.46522e-5
MA0105.10.0737
MA0106.10.34
MA0107.10.00775
MA0108.20.346
MA0111.10.545
MA0112.20.789
MA0113.10.256
MA0114.10.0611
MA0115.10.239
MA0116.10.121
MA0117.10.679
MA0119.10.986
MA0122.10.132
MA0124.10.608
MA0125.10.951
MA0131.10.235
MA0135.10.0487
MA0136.12.64754e-11
MA0137.20.112
MA0138.20.417
MA0139.10.364
MA0140.10.768
MA0141.10.712
MA0142.10.906
MA0143.10.42
MA0144.10.241
MA0145.10.501
MA0146.10.853
MA0147.11.95343e-4
MA0148.10.513
MA0149.10.458
MA0150.10.151
MA0152.10.0391
MA0153.10.583
MA0154.10.146
MA0155.10.76
MA0156.15.48295e-8
MA0157.10.0519
MA0159.10.00255
MA0160.10.484
MA0162.10.184
MA0163.10.0693
MA0164.10.359
MA0258.10.777
MA0259.10.0436



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: CNhs12493

Novel motifP-value
10.241
100.196
1000.153
1010.298
1020.0212
1030.878
1040.546
1050.702
1060.872
1070.079
1080.633
1090.603
110.706
1100.495
1110.297
1120.745
1130.472
1140.333
1150.559
1160.457
1170.0291
1180.0686
1190.518
120.322
1200.479
1210.764
1220.067
1230.0101
1240.713
1250.942
1260.157
1270.834
1280.193
1290.567
130.0348
1300.134
1310.963
1320.576
1330.612
1340.0389
1350.912
1360.86
1370.593
1380.463
1390.00324
140.221
1400.907
1410.0159
1420.658
1430.639
1440.981
1450.781
1460.631
1470.246
1480.402
1490.488
150.239
1500.461
1510.57
1520.0593
1530.995
1540.663
1556.96266e-4
1560.906
1570.0605
1580.00783
1590.463
160.662
1600.853
1610.359
1620.12
1630.64
1640.0232
1650.176
1660.0454
1670.375
1680.406
1690.594
170.916
180.365
190.248
20.236
200.154
210.839
220.608
230.304
240.557
250.328
260.624
270.733
280.188
290.0353
30.335
300.147
310.974
323.1588e-7
330.94
340.966
350.197
360.048
370.633
380.218
390.924
40.85
400.164
410.766
420.476
430.443
440.222
450.844
460.973
470.191
480.45
490.255
50.899
500.772
510.985
520.615
530.462
540.948
550.608
560.897
570.915
580.229
590.402
60.689
600.575
610.58
620.58
630.9
640.166
650.901
660.222
670.298
680.214
690.864
70.141
700.35
710.307
720.199
730.614
740.41
750.167
760.0968
770.321
780.0726
790.016
80.959
800.998
810.638
820.529
830.277
840.689
850.42
860.558
870.446
880.532
890.15
90.333
900.513
910.695
920.498
930.813
940.738
950.753
960.53
970.428
980.037
990.00183



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: CNhs12493


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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