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FF:11556-120C8: 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 16:47, 29 March 2012


Name:Fibroblast - skin dystrophia myotonica, donor1
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
sexF
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-0.0306
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-0.221
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: CNhs11353

Jaspar motifP-value
MA0002.20.289
MA0003.10.931
MA0004.10.0172
MA0006.10.302
MA0007.10.327
MA0009.10.0291
MA0014.10.446
MA0017.10.0979
MA0018.23.6589e-5
MA0019.10.854
MA0024.12.91578e-5
MA0025.10.0342
MA0027.10.68
MA0028.10.0587
MA0029.10.615
MA0030.10.706
MA0031.10.936
MA0035.20.0125
MA0038.10.207
MA0039.20.00301
MA0040.10.453
MA0041.10.461
MA0042.10.589
MA0043.13.70601e-4
MA0046.10.832
MA0047.20.792
MA0048.10.0759
MA0050.10.0512
MA0051.10.371
MA0052.10.0266
MA0055.10.562
MA0057.10.995
MA0058.10.00187
MA0059.10.0702
MA0060.11.38105e-7
MA0061.10.00734
MA0062.22.71539e-7
MA0065.20.0469
MA0066.10.939
MA0067.10.00573
MA0068.10.442
MA0069.10.116
MA0070.10.77
MA0071.10.355
MA0072.10.422
MA0073.10.538
MA0074.10.997
MA0076.10.122
MA0077.10.413
MA0078.10.44
MA0079.20.515
MA0080.26.21e-9
MA0081.10.008
MA0083.10.0485
MA0084.10.183
MA0087.10.732
MA0088.10.646
MA0090.15.91176e-6
MA0091.10.0608
MA0092.10.249
MA0093.10.0228
MA0099.20.00911
MA0100.10.304
MA0101.14.47622e-5
MA0102.20.503
MA0103.14.7804e-5
MA0104.22.05663e-4
MA0105.10.141
MA0106.10.0501
MA0107.14.23399e-4
MA0108.20.972
MA0111.10.222
MA0112.20.245
MA0113.10.946
MA0114.10.0463
MA0115.10.0677
MA0116.10.684
MA0117.10.675
MA0119.10.57
MA0122.10.518
MA0124.10.79
MA0125.10.681
MA0131.10.726
MA0135.10.0782
MA0136.11.09955e-9
MA0137.20.803
MA0138.20.445
MA0139.10.447
MA0140.10.0379
MA0141.10.0978
MA0142.10.022
MA0143.10.827
MA0144.10.876
MA0145.10.767
MA0146.10.548
MA0147.16.23353e-4
MA0148.10.941
MA0149.10.405
MA0150.10.00477
MA0152.10.0168
MA0153.10.678
MA0154.10.884
MA0155.10.567
MA0156.11.8889e-6
MA0157.10.931
MA0159.10.751
MA0160.10.00606
MA0162.10.121
MA0163.10.595
MA0164.10.798
MA0258.10.575
MA0259.10.248



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: CNhs11353

Novel motifP-value
10.251
100.376
1000.583
1010.378
1020.0231
1030.747
1040.782
1050.159
1060.275
1070.93
1080.671
1090.203
110.245
1100.766
1110.406
1120.733
1130.0382
1140.624
1150.267
1160.52
1170.033
1180.323
1190.15
120.454
1200.844
1210.503
1220.219
1230.00141
1240.558
1250.407
1260.64
1270.768
1280.633
1290.33
130.225
1300.543
1310.929
1320.584
1330.934
1340.419
1350.288
1360.264
1370.296
1380.748
1390.721
140.216
1400.908
1410.212
1420.746
1430.756
1440.392
1450.9
1460.618
1470.0811
1480.154
1490.0373
150.26
1500.354
1510.579
1520.41
1530.345
1540.434
1550.0409
1560.692
1570.203
1580.00889
1590.793
160.149
1600.686
1610.369
1620.372
1630.635
1640.809
1650.504
1660.0896
1670.175
1680.602
1690.201
170.727
180.126
190.0301
20.999
200.52
210.0305
220.673
230.543
240.417
250.214
260.896
270.896
280.472
290.73
30.752
300.25
310.652
327.02516e-15
330.562
340.788
350.875
360.0767
370.612
380.295
390.489
40.736
400.053
410.743
420.476
430.821
440.57
450.733
460.928
470.294
480.479
490.297
50.57
500.849
510.592
520.976
530.0978
540.835
550.214
560.628
570.944
580.117
590.375
60.679
600.298
610.21
620.394
630.901
640.32
650.607
660.215
670.973
680.425
690.783
70.0712
700.508
710.639
720.604
730.585
740.111
750.192
760.71
770.255
780.0995
790.0171
80.812
800.733
810.796
820.358
830.318
840.115
850.699
860.729
870.621
880.36
890.455
90.879
900.743
910.708
920.5
930.976
940.873
950.193
960.627
970.62
980.332
990.0167



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: CNhs11353


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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