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FF:11557-120C9: 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, 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
age50 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-0.0214
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-0.0297
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: CNhs11354

Jaspar motifP-value
MA0002.20.471
MA0003.10.863
MA0004.10.0252
MA0006.10.506
MA0007.10.575
MA0009.10.284
MA0014.10.24
MA0017.10.397
MA0018.22.45197e-6
MA0019.10.769
MA0024.10.00643
MA0025.10.014
MA0027.10.824
MA0028.10.194
MA0029.10.341
MA0030.10.177
MA0031.10.291
MA0035.20.0154
MA0038.10.0182
MA0039.20.00456
MA0040.10.316
MA0041.10.772
MA0042.10.866
MA0043.14.60705e-4
MA0046.10.728
MA0047.20.413
MA0048.10.0173
MA0050.10.18
MA0051.10.827
MA0052.10.544
MA0055.10.756
MA0057.10.308
MA0058.10.00364
MA0059.10.568
MA0060.11.43701e-8
MA0061.10.0541
MA0062.21.84763e-6
MA0065.20.327
MA0066.10.512
MA0067.10.00554
MA0068.10.366
MA0069.10.0692
MA0070.10.76
MA0071.10.75
MA0072.10.392
MA0073.10.653
MA0074.10.503
MA0076.10.104
MA0077.10.0517
MA0078.10.681
MA0079.20.0764
MA0080.21.20892e-8
MA0081.10.0136
MA0083.10.00461
MA0084.10.921
MA0087.10.989
MA0088.10.911
MA0090.11.24864e-5
MA0091.10.0799
MA0092.10.0168
MA0093.10.0377
MA0099.20.315
MA0100.10.567
MA0101.19.10444e-4
MA0102.20.533
MA0103.16.45547e-5
MA0104.20.0521
MA0105.10.262
MA0106.10.0129
MA0107.10.00309
MA0108.20.214
MA0111.10.081
MA0112.20.00768
MA0113.10.447
MA0114.10.282
MA0115.10.198
MA0116.10.541
MA0117.10.974
MA0119.10.271
MA0122.10.75
MA0124.10.868
MA0125.10.329
MA0131.10.971
MA0135.10.0517
MA0136.11.01745e-9
MA0137.20.908
MA0138.20.612
MA0139.10.962
MA0140.10.163
MA0141.10.855
MA0142.10.228
MA0143.10.585
MA0144.10.906
MA0145.10.246
MA0146.10.698
MA0147.10.369
MA0148.10.785
MA0149.10.927
MA0150.10.0928
MA0152.10.0251
MA0153.10.245
MA0154.10.799
MA0155.10.833
MA0156.13.13762e-6
MA0157.10.868
MA0159.10.865
MA0160.10.0546
MA0162.10.278
MA0163.10.0383
MA0164.10.826
MA0258.10.798
MA0259.10.69



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: CNhs11354

Novel motifP-value
10.953
100.65
1000.88
1010.477
1020.0443
1030.949
1040.787
1050.162
1060.64
1070.67
1080.45
1090.409
110.675
1100.965
1110.497
1120.553
1130.00249
1140.478
1150.582
1160.266
1170.28
1180.66
1190.318
120.375
1200.738
1210.765
1220.0717
1234.30511e-4
1240.803
1250.414
1260.898
1270.947
1280.815
1290.378
130.82
1300.426
1310.97
1320.363
1330.196
1340.273
1350.238
1360.0796
1370.159
1380.827
1390.917
140.196
1400.347
1410.187
1420.858
1430.966
1440.331
1450.558
1460.688
1470.0737
1480.401
1490.0186
150.615
1500.382
1510.841
1520.732
1530.247
1540.583
1550.0528
1560.653
1570.658
1580.00715
1590.844
160.0333
1600.263
1610.196
1620.534
1630.677
1640.469
1650.501
1660.148
1670.686
1680.865
1690.0532
170.55
180.046
190.00764
20.541
200.363
210.0225
220.282
230.164
240.308
250.356
260.836
270.836
280.298
290.849
30.572
300.211
310.657
329.06456e-14
330.543
340.773
350.967
360.122
370.146
380.271
390.354
40.541
400.123
410.686
420.642
430.987
440.502
450.396
460.772
470.422
480.425
490.774
50.506
500.549
510.711
520.838
530.112
540.723
550.175
560.921
570.959
580.192
590.307
60.947
600.493
610.579
620.967
630.583
640.381
650.937
660.289
670.694
680.993
690.962
70.217
700.746
710.331
720.966
730.431
740.0727
750.929
760.688
770.154
780.262
790.0516
80.56
800.497
810.891
820.704
830.314
840.28
850.742
860.691
870.971
880.591
890.0883
90.866
900.778
910.984
920.153
930.737
940.209
950.747
960.927
970.703
980.148
990.0106



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: CNhs11354


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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