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FF:11238-116D5: 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 16:35, 29 March 2012


Name:Fibroblast - Periodontal Ligament, donor1
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 number1229
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-0.105
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-lymphoma0.631
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: CNhs10867

Jaspar motifP-value
MA0002.20.0179
MA0003.10.271
MA0004.10.375
MA0006.10.795
MA0007.10.457
MA0009.10.812
MA0014.10.175
MA0017.10.032
MA0018.20.0024
MA0019.10.065
MA0024.18.06356e-11
MA0025.10.00566
MA0027.10.52
MA0028.10.00478
MA0029.10.445
MA0030.10.14
MA0031.10.179
MA0035.20.0128
MA0038.15.27995e-6
MA0039.20.281
MA0040.10.444
MA0041.10.18
MA0042.10.582
MA0043.10.00147
MA0046.10.749
MA0047.20.539
MA0048.15.58281e-4
MA0050.11.6113e-4
MA0051.10.00377
MA0052.10.444
MA0055.14.0317e-5
MA0057.10.988
MA0058.10.228
MA0059.10.851
MA0060.13.86453e-13
MA0061.11.54949e-4
MA0062.20.787
MA0065.20.0343
MA0066.10.681
MA0067.10.0172
MA0068.10.362
MA0069.10.283
MA0070.10.935
MA0071.10.963
MA0072.10.74
MA0073.10.23
MA0074.10.329
MA0076.10.0192
MA0077.10.678
MA0078.10.59
MA0079.20.0077
MA0080.23.25551e-12
MA0081.10.0863
MA0083.10.126
MA0084.10.0167
MA0087.10.534
MA0088.12.3556e-4
MA0090.10.152
MA0091.10.334
MA0092.10.686
MA0093.10.327
MA0099.20.917
MA0100.10.0621
MA0101.10.00347
MA0102.20.00233
MA0103.12.36139e-4
MA0104.20.651
MA0105.10.11
MA0106.10.454
MA0107.12.23011e-5
MA0108.20.0168
MA0111.10.903
MA0112.20.193
MA0113.10.77
MA0114.10.236
MA0115.10.722
MA0116.10.323
MA0117.10.486
MA0119.10.257
MA0122.10.457
MA0124.10.175
MA0125.10.22
MA0131.10.111
MA0135.10.0983
MA0136.11.89127e-8
MA0137.20.641
MA0138.20.256
MA0139.10.904
MA0140.10.389
MA0141.10.615
MA0142.10.538
MA0143.10.719
MA0144.10.299
MA0145.10.165
MA0146.10.599
MA0147.10.717
MA0148.10.516
MA0149.10.449
MA0150.10.0419
MA0152.10.00126
MA0153.10.259
MA0154.10.0347
MA0155.10.0646
MA0156.15.65251e-4
MA0157.10.216
MA0159.10.00553
MA0160.10.188
MA0162.10.128
MA0163.10.84
MA0164.10.146
MA0258.10.114
MA0259.10.277



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: CNhs10867

Novel motifP-value
10.653
100.251
1000.353
1010.995
1020.295
1030.128
1040.739
1050.626
1061.26575e-4
1070.219
1080.203
1090.957
110.702
1100.194
1110.906
1120.0588
1130.188
1140.0735
1150.54
1160.61
1170.485
1180.842
1190.332
120.858
1200.903
1210.739
1220.0575
1230.493
1240.995
1250.363
1260.938
1270.7
1280.0345
1290.516
130.582
1300.00508
1310.471
1320.582
1330.596
1340.0875
1350.0186
1360.764
1370.188
1380.141
1397.19341e-7
140.302
1400.662
1410.285
1420.331
1430.246
1440.648
1450.375
1460.873
1470.158
1480.234
1490.191
150.356
1500.954
1510.142
1520.0275
1530.855
1540.982
1550.0433
1560.605
1570.108
1580.101
1590.203
160.462
1600.289
1610.787
1620.311
1630.648
1640.797
1650.576
1660.817
1670.63
1680.172
1690.254
170.264
180.672
190.705
20.228
200.277
210.0495
220.513
230.0429
240.288
250.444
260.397
270.133
280.458
290.619
30.855
300.592
310.637
320.848
330.257
340.395
350.32
360.929
370.648
380.42
390.961
40.0927
400.773
410.0377
420.678
430.457
440.312
450.0814
460.829
470.861
480.715
490.492
50.282
500.284
510.65
520.0545
530.663
540.68
550.47
560.963
570.638
580.0826
590.209
60.598
600.0094
610.668
620.0869
630.682
640.803
650.0913
660.012
670.655
680.608
690.425
70.471
700.0552
710.879
720.434
730.196
740.26
750.728
760.686
770.544
780.737
790.375
80.862
800.0932
810.667
820.0119
830.888
840.536
850.0141
860.207
870.905
880.203
890.171
90.468
900.708
910.889
920.0621
930.626
940.444
950.728
960.838
970.924
980.338
990.00562



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: CNhs10867


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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