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FF:11454-119A5: 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, donor5
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 number4823
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-0.113
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-lymphoma0.533
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: CNhs12055

Jaspar motifP-value
MA0002.20.0465
MA0003.10.339
MA0004.10.574
MA0006.10.507
MA0007.10.49
MA0009.10.383
MA0014.10.903
MA0017.10.0998
MA0018.20.131
MA0019.10.356
MA0024.12.28299e-9
MA0025.10.337
MA0027.10.628
MA0028.10.0059
MA0029.10.447
MA0030.10.0182
MA0031.10.0155
MA0035.20.0358
MA0038.10.00153
MA0039.20.462
MA0040.10.575
MA0041.10.241
MA0042.10.312
MA0043.10.0123
MA0046.10.949
MA0047.20.65
MA0048.11.77699e-4
MA0050.17.99237e-8
MA0051.14.93849e-6
MA0052.10.919
MA0055.11.42895e-4
MA0057.10.486
MA0058.10.797
MA0059.10.2
MA0060.11.14632e-10
MA0061.10.00522
MA0062.20.277
MA0065.20.0547
MA0066.10.779
MA0067.10.18
MA0068.10.294
MA0069.10.613
MA0070.10.383
MA0071.10.656
MA0072.10.884
MA0073.10.785
MA0074.10.56
MA0076.10.00959
MA0077.10.72
MA0078.10.913
MA0079.20.134
MA0080.26.13827e-12
MA0081.10.112
MA0083.10.639
MA0084.10.152
MA0087.10.524
MA0088.19.4015e-4
MA0090.10.606
MA0091.10.403
MA0092.10.528
MA0093.10.63
MA0099.20.891
MA0100.10.0501
MA0101.10.0566
MA0102.27.67054e-4
MA0103.11.13031e-4
MA0104.20.0314
MA0105.10.0447
MA0106.10.204
MA0107.10.00318
MA0108.20.156
MA0111.10.688
MA0112.20.0162
MA0113.10.938
MA0114.10.197
MA0115.10.959
MA0116.10.144
MA0117.10.813
MA0119.10.758
MA0122.10.32
MA0124.10.483
MA0125.10.225
MA0131.10.159
MA0135.10.715
MA0136.15.32639e-7
MA0137.20.079
MA0138.20.848
MA0139.10.303
MA0140.10.298
MA0141.10.903
MA0142.10.342
MA0143.10.501
MA0144.10.0518
MA0145.10.0261
MA0146.10.339
MA0147.10.0427
MA0148.10.434
MA0149.10.981
MA0150.10.185
MA0152.10.0283
MA0153.10.279
MA0154.10.00886
MA0155.10.126
MA0156.10.0247
MA0157.10.0469
MA0159.10.0138
MA0160.10.273
MA0162.10.336
MA0163.10.841
MA0164.10.655
MA0258.10.0375
MA0259.10.0767



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: CNhs12055

Novel motifP-value
10.716
100.178
1000.573
1010.608
1020.445
1030.0276
1040.792
1050.575
1060.00355
1070.194
1080.225
1090.888
110.973
1100.421
1110.948
1120.0535
1130.0106
1140.228
1150.866
1160.389
1170.8
1180.683
1190.0973
120.512
1200.178
1210.655
1220.119
1230.402
1240.156
1250.654
1260.841
1270.605
1280.0322
1290.0943
130.937
1300.00733
1310.53
1320.865
1330.989
1340.517
1350.0492
1360.237
1370.0455
1380.0972
1393.41692e-5
140.0827
1400.8
1410.791
1420.541
1430.59
1440.519
1450.425
1460.707
1470.457
1480.412
1490.236
150.264
1500.79
1510.207
1520.13
1530.47
1540.457
1550.0536
1560.547
1570.0976
1580.0288
1590.0319
160.635
1600.479
1610.879
1620.677
1630.563
1640.773
1650.138
1660.958
1670.643
1680.48
1690.0911
170.404
180.686
190.777
20.51
200.196
210.137
220.268
230.036
240.656
250.775
260.328
270.521
280.334
290.916
30.722
300.403
310.451
320.816
330.478
340.327
350.477
360.664
370.545
380.345
390.725
40.11
400.48
410.256
420.865
430.22
440.628
450.045
460.486
470.954
480.618
490.263
50.122
500.571
510.61
520.186
530.341
540.608
550.737
560.764
570.778
580.131
590.378
60.697
600.0331
610.989
620.243
630.975
640.708
650.155
660.0758
670.791
680.707
690.663
70.424
700.00671
710.983
720.176
730.501
740.225
750.473
760.955
770.777
780.71
790.696
80.81
800.0634
810.375
820.0081
830.213
840.967
850.013
860.464
870.129
880.322
890.169
90.692
900.627
910.46
920.252
930.724
940.951
950.242
960.303
970.88
980.225
990.0632



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: CNhs12055


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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