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FF:11560-120D3: 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 17:01, 29 March 2012


Name:Fibroblast - skin dystrophia myotonica, donor3
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
age18 year old adult
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-0.113
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-lymphoma0.162
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
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: CNhs11913

Jaspar motifP-value
MA0002.20.187
MA0003.10.739
MA0004.10.0108
MA0006.10.433
MA0007.10.503
MA0009.10.374
MA0014.10.495
MA0017.10.083
MA0018.21.82619e-6
MA0019.10.744
MA0024.10.702
MA0025.10.0866
MA0027.10.499
MA0028.10.224
MA0029.10.328
MA0030.10.56
MA0031.10.954
MA0035.20.00904
MA0038.10.251
MA0039.20.019
MA0040.10.339
MA0041.10.589
MA0042.10.794
MA0043.10.00625
MA0046.10.926
MA0047.20.924
MA0048.10.0327
MA0050.10.227
MA0051.10.689
MA0052.10.488
MA0055.10.337
MA0057.10.409
MA0058.10.00546
MA0059.10.0704
MA0060.10.00196
MA0061.10.015
MA0062.20.174
MA0065.20.0574
MA0066.10.829
MA0067.10.00588
MA0068.10.878
MA0069.10.206
MA0070.10.649
MA0071.10.333
MA0072.10.674
MA0073.10.823
MA0074.10.988
MA0076.10.14
MA0077.10.2
MA0078.10.398
MA0079.20.813
MA0080.22.03326e-8
MA0081.10.102
MA0083.10.135
MA0084.10.161
MA0087.10.719
MA0088.10.421
MA0090.11.65578e-4
MA0091.10.0776
MA0092.10.237
MA0093.10.025
MA0099.20.953
MA0100.10.883
MA0101.10.00149
MA0102.20.744
MA0103.16.53335e-6
MA0104.20.0051
MA0105.10.141
MA0106.10.0275
MA0107.14.9867e-4
MA0108.20.88
MA0111.10.0697
MA0112.20.463
MA0113.10.876
MA0114.10.0521
MA0115.10.081
MA0116.10.987
MA0117.10.703
MA0119.10.807
MA0122.10.55
MA0124.10.987
MA0125.10.549
MA0131.10.825
MA0135.10.913
MA0136.12.81531e-6
MA0137.20.672
MA0138.20.918
MA0139.10.657
MA0140.10.041
MA0141.10.135
MA0142.10.00919
MA0143.10.731
MA0144.10.788
MA0145.10.76
MA0146.10.893
MA0147.10.039
MA0148.10.856
MA0149.10.55
MA0150.10.229
MA0152.10.0325
MA0153.10.285
MA0154.10.886
MA0155.10.563
MA0156.10.0226
MA0157.10.853
MA0159.10.266
MA0160.10.0203
MA0162.10.295
MA0163.10.041
MA0164.10.718
MA0258.10.164
MA0259.10.431



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: CNhs11913

Novel motifP-value
10.525
100.948
1000.399
1010.242
1020.0377
1030.826
1040.677
1050.375
1060.0605
1070.469
1080.701
1090.7
110.557
1100.64
1110.121
1120.968
1139.16156e-4
1140.907
1150.326
1160.615
1170.972
1180.765
1190.143
120.32
1200.591
1210.508
1220.114
1232.09756e-5
1240.964
1250.83
1260.533
1270.452
1280.139
1290.509
130.311
1300.0821
1310.635
1320.497
1330.679
1340.39
1350.44
1360.152
1370.371
1380.424
1390.0422
140.291
1400.293
1410.0757
1420.841
1430.574
1440.77
1450.768
1460.652
1470.136
1480.0548
1490.101
150.127
1500.372
1510.238
1520.365
1530.366
1540.754
1550.00409
1560.673
1570.217
1580.00256
1590.363
160.428
1600.792
1610.388
1620.658
1630.858
1640.993
1650.0804
1660.0571
1670.348
1680.558
1690.111
170.894
180.353
190.0432
20.413
200.48
210.148
220.382
230.886
240.918
250.305
260.488
270.951
280.504
290.948
30.88
300.138
310.717
321.68831e-9
330.58
340.971
350.444
360.0399
370.191
380.297
390.543
40.418
400.0217
410.558
420.72
430.259
440.547
450.569
460.816
470.462
480.544
490.0749
50.76
500.607
510.743
520.53
530.223
540.781
550.19
560.868
570.884
580.11
590.531
60.266
600.124
610.766
620.317
630.754
640.422
650.578
660.848
670.642
680.944
690.734
70.11
700.361
710.69
720.434
730.393
740.246
750.726
760.955
770.212
780.102
790.0857
80.695
800.798
810.37
820.472
830.0952
840.38
850.265
860.473
870.373
880.559
890.787
90.552
900.656
910.568
920.541
930.783
940.787
950.738
960.909
970.484
980.105
990.0143



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: CNhs11913


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)

DOID: Disease
0080000 (muscular disease)
11722 (myotonic dystrophy)
17 (musculoskeletal system disease)
4 (disease)
423 (myopathy)
450 (myotonic disease)
66 (muscle tissue disease)
7 (disease of anatomical entity)

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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