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FF:11458-119A9: 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 17:09, 29 March 2012


Name:Fibroblast - Dermal, donor6
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueskin
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 number4828
catalog numberSC2305
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-0.121
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-lymphoma0.596
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
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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: CNhs12059

Jaspar motifP-value
MA0002.20.0539
MA0003.10.236
MA0004.10.728
MA0006.10.539
MA0007.10.724
MA0009.10.286
MA0014.10.724
MA0017.10.0681
MA0018.20.146
MA0019.10.559
MA0024.12.98111e-11
MA0025.10.0764
MA0027.10.537
MA0028.10.00517
MA0029.10.733
MA0030.10.00859
MA0031.10.0267
MA0035.20.012
MA0038.10.00294
MA0039.20.776
MA0040.10.141
MA0041.10.174
MA0042.10.333
MA0043.10.0159
MA0046.10.592
MA0047.20.411
MA0048.12.89754e-4
MA0050.14.7093e-7
MA0051.14.95436e-6
MA0052.10.976
MA0055.13.40222e-5
MA0057.10.73
MA0058.10.765
MA0059.10.301
MA0060.12.96454e-12
MA0061.10.00352
MA0062.20.152
MA0065.20.0498
MA0066.10.625
MA0067.10.168
MA0068.10.537
MA0069.10.425
MA0070.10.381
MA0071.10.785
MA0072.10.931
MA0073.10.508
MA0074.10.394
MA0076.10.00575
MA0077.10.6
MA0078.10.651
MA0079.20.15
MA0080.22.92671e-12
MA0081.10.209
MA0083.10.746
MA0084.10.0995
MA0087.10.407
MA0088.12.75715e-4
MA0090.10.6
MA0091.10.378
MA0092.10.478
MA0093.10.691
MA0099.20.528
MA0100.10.0779
MA0101.10.0922
MA0102.21.35654e-4
MA0103.13.53368e-5
MA0104.20.0356
MA0105.10.08
MA0106.10.359
MA0107.10.00384
MA0108.20.0579
MA0111.10.992
MA0112.20.00972
MA0113.10.919
MA0114.10.243
MA0115.10.933
MA0116.10.267
MA0117.10.925
MA0119.10.87
MA0122.10.526
MA0124.10.7
MA0125.10.411
MA0131.10.132
MA0135.10.999
MA0136.17.19189e-7
MA0137.20.0979
MA0138.20.818
MA0139.10.317
MA0140.10.201
MA0141.10.955
MA0142.10.417
MA0143.10.506
MA0144.10.0576
MA0145.10.0353
MA0146.10.515
MA0147.10.0628
MA0148.10.252
MA0149.10.848
MA0150.10.221
MA0152.10.0621
MA0153.10.312
MA0154.10.0164
MA0155.10.0623
MA0156.10.0161
MA0157.10.0361
MA0159.10.0352
MA0160.10.199
MA0162.10.387
MA0163.10.602
MA0164.10.471
MA0258.10.0273
MA0259.10.0686



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: CNhs12059

Novel motifP-value
10.706
100.204
1000.601
1010.381
1020.346
1030.0767
1040.987
1050.708
1065.97005e-4
1070.171
1080.216
1090.908
110.784
1100.484
1110.521
1120.0534
1130.0279
1140.25
1150.776
1160.432
1170.674
1180.896
1190.126
120.483
1200.241
1210.994
1220.11
1230.784
1240.392
1250.569
1260.851
1270.619
1280.0171
1290.144
130.684
1300.0186
1310.766
1320.934
1330.74
1340.582
1350.0106
1360.5
1370.179
1380.251
1399.22491e-6
140.179
1400.839
1410.701
1420.536
1430.335
1440.683
1450.397
1460.717
1470.539
1480.338
1490.208
150.283
1500.982
1510.418
1520.0618
1530.261
1540.427
1550.0826
1560.684
1570.183
1580.0292
1590.0295
160.626
1600.523
1610.458
1620.815
1630.904
1640.76
1650.255
1660.87
1670.576
1680.445
1690.104
170.399
180.817
190.515
20.559
200.21
210.0442
220.241
230.0351
240.439
250.988
260.327
270.471
280.554
290.983
30.691
300.383
310.489
320.605
330.426
340.263
350.453
360.874
370.448
380.41
390.933
40.138
400.539
410.135
420.979
430.222
440.766
450.0648
460.498
470.833
480.573
490.3
50.162
500.614
510.661
520.0932
530.547
540.499
550.708
560.753
570.54
580.126
590.226
60.748
600.0177
610.963
620.177
630.862
640.932
650.158
660.057
670.788
680.994
690.743
70.495
700.00218
710.96
720.179
730.468
740.143
750.597
760.703
770.544
780.834
790.597
80.965
800.0292
810.357
820.0126
830.385
840.778
850.00614
860.426
870.176
880.379
890.1
90.531
900.62
910.545
920.176
930.826
940.863
950.249
960.369
970.752
980.448
990.0789



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: CNhs12059


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)
0002551 (fibroblast of dermis)
0002620 (skin fibroblast)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002067 (dermis)
0002097 (skin of body)
0002199 (integument)
0002329 (somite)
0002384 (connective tissue)
0002416 (integumental system)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003102 (surface structure)
0003104 (mesenchyme)
0004016 (dermatome)
0004120 (mesoderm-derived structure)
0004290 (dermomyotome)
0004923 (organ component layer)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0009142 (entire embryonic mesenchyme)

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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