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FF:11558-120D1: 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 17:00, 29 March 2012


Name:Fibroblast - skin spinal muscular atrophy, donor2
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 stageNA
sexM
age2 year old child
cell typefibroblast
cell lineNA
companyCoriell
collaborationSplicing (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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-0.0465
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-0.125
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
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: CNhs11911

Jaspar motifP-value
MA0002.20.0144
MA0003.10.386
MA0004.10.00497
MA0006.10.34
MA0007.10.39
MA0009.10.25
MA0014.10.535
MA0017.10.0947
MA0018.29.83891e-6
MA0019.10.539
MA0024.10.0842
MA0025.11.5017e-4
MA0027.10.641
MA0028.10.431
MA0029.10.511
MA0030.10.592
MA0031.10.866
MA0035.20.0518
MA0038.10.0644
MA0039.20.15
MA0040.10.35
MA0041.10.16
MA0042.10.082
MA0043.18.17319e-4
MA0046.10.41
MA0047.20.824
MA0048.10.183
MA0050.10.89
MA0051.10.0146
MA0052.10.0233
MA0055.10.46
MA0057.10.619
MA0058.16.95672e-4
MA0059.10.00818
MA0060.17.02431e-8
MA0061.10.0023
MA0062.20.0274
MA0065.20.0352
MA0066.10.654
MA0067.12.04541e-4
MA0068.10.616
MA0069.10.0963
MA0070.10.975
MA0071.10.367
MA0072.10.539
MA0073.10.598
MA0074.10.761
MA0076.10.365
MA0077.10.442
MA0078.10.412
MA0079.20.683
MA0080.21.28202e-10
MA0081.10.087
MA0083.10.911
MA0084.10.142
MA0087.10.315
MA0088.10.451
MA0090.10.00537
MA0091.10.0555
MA0092.10.372
MA0093.10.00732
MA0099.23.77207e-6
MA0100.10.132
MA0101.17.18559e-5
MA0102.20.862
MA0103.12.81195e-4
MA0104.20.00143
MA0105.10.11
MA0106.10.287
MA0107.14.42757e-4
MA0108.20.233
MA0111.10.358
MA0112.20.752
MA0113.10.731
MA0114.10.0399
MA0115.10.0139
MA0116.10.384
MA0117.10.114
MA0119.10.727
MA0122.10.923
MA0124.10.935
MA0125.10.915
MA0131.10.647
MA0135.10.598
MA0136.15.64425e-9
MA0137.20.097
MA0138.20.692
MA0139.10.591
MA0140.10.0497
MA0141.10.169
MA0142.10.301
MA0143.10.471
MA0144.10.43
MA0145.10.662
MA0146.10.581
MA0147.10.00205
MA0148.10.407
MA0149.10.332
MA0150.10.00266
MA0152.10.00557
MA0153.10.109
MA0154.10.832
MA0155.10.857
MA0156.14.24571e-5
MA0157.10.921
MA0159.10.351
MA0160.10.037
MA0162.10.0971
MA0163.10.116
MA0164.10.757
MA0258.10.167
MA0259.10.0477



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: CNhs11911

Novel motifP-value
10.096
100.331
1000.766
1010.432
1020.0951
1030.817
1040.996
1050.384
1060.00914
1070.215
1080.64
1090.225
110.408
1100.674
1110.0427
1120.846
1130.258
1140.99
1150.344
1160.41
1170.906
1180.859
1190.0301
120.275
1200.961
1210.475
1220.0824
1236.58233e-4
1240.439
1250.456
1260.365
1270.424
1280.223
1290.396
130.38
1300.489
1310.794
1320.135
1330.245
1340.245
1350.539
1360.4
1370.0233
1380.304
1390.0514
140.38
1400.837
1410.101
1420.526
1430.0571
1440.175
1450.376
1460.77
1470.304
1480.0371
1490.201
150.129
1500.905
1510.563
1520.779
1530.126
1540.235
1550.0729
1560.711
1570.328
1580.00337
1590.908
160.363
1600.959
1610.874
1620.868
1630.916
1640.148
1650.322
1660.0347
1670.454
1680.441
1690.231
170.595
180.93
190.0271
20.395
200.595
210.697
220.26
230.819
240.354
250.223
260.694
270.756
280.619
290.696
30.797
300.0848
310.816
321.1402e-10
330.374
340.688
350.426
360.0255
370.514
380.441
390.584
40.113
400.041
410.0194
420.6
430.391
440.969
450.692
460.601
470.255
480.444
490.179
50.578
500.607
510.983
520.478
530.447
540.8
550.204
560.732
570.382
580.118
590.727
60.795
600.121
610.424
620.239
630.752
640.457
650.669
660.102
670.3
680.981
690.709
70.107
700.8
710.198
720.686
730.767
740.792
750.879
760.538
770.46
780.0903
794.61789e-4
80.637
800.596
810.25
820.875
830.0749
840.214
850.714
860.694
870.789
880.284
890.245
90.734
900.294
910.476
920.784
930.583
940.98
950.0939
960.365
970.592
980.432
990.0435



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: CNhs11911


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)
0002620 (skin fibroblast)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0001062 (anatomical entity)
0002097 (skin of body)
0002199 (integument)
0002384 (connective tissue)
0002416 (integumental system)
0003102 (surface structure)

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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