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FF:14326-155E6: 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 17:19, 29 March 2012


Name:Fibroblast - skin spinal muscular atrophy, donor1 (nuclear fraction)
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
age3 year old child
cell typefibroblast
cell lineNA
companyCoriell
collaborationFANTOM5 OSC CORE (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-0.111
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-lymphoma0.357
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C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
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: CNhs12404

Jaspar motifP-value
MA0002.20.00521
MA0003.10.00159
MA0004.10.0646
MA0006.10.8
MA0007.10.478
MA0009.10.315
MA0014.10.309
MA0017.10.00163
MA0018.20.424
MA0019.10.802
MA0024.10.35
MA0025.10.0616
MA0027.10.554
MA0028.10.0502
MA0029.10.475
MA0030.10.169
MA0031.10.113
MA0035.25.46741e-5
MA0038.10.906
MA0039.20.136
MA0040.10.518
MA0041.10.339
MA0042.10.777
MA0043.10.362
MA0046.10.198
MA0047.20.396
MA0048.14.61887e-4
MA0050.10.285
MA0051.10.103
MA0052.10.261
MA0055.10.0922
MA0057.10.948
MA0058.10.0195
MA0059.10.0454
MA0060.10.576
MA0061.19.87221e-4
MA0062.20.31
MA0065.24.4943e-4
MA0066.10.0959
MA0067.10.949
MA0068.10.218
MA0069.10.0145
MA0070.10.287
MA0071.10.0607
MA0072.10.0923
MA0073.10.822
MA0074.10.358
MA0076.10.0111
MA0077.10.14
MA0078.10.17
MA0079.20.125
MA0080.25.1445e-9
MA0081.10.055
MA0083.18.87447e-4
MA0084.10.676
MA0087.10.115
MA0088.10.708
MA0090.10.00104
MA0091.10.492
MA0092.10.731
MA0093.10.0779
MA0099.20.153
MA0100.10.541
MA0101.10.00277
MA0102.20.528
MA0103.17.25543e-6
MA0104.20.00117
MA0105.19.81814e-4
MA0106.10.5
MA0107.12.4981e-4
MA0108.20.297
MA0111.10.0765
MA0112.20.12
MA0113.10.731
MA0114.10.0012
MA0115.10.174
MA0116.10.681
MA0117.10.533
MA0119.10.487
MA0122.10.369
MA0124.10.3
MA0125.10.172
MA0131.10.19
MA0135.10.553
MA0136.13.35283e-5
MA0137.20.564
MA0138.20.374
MA0139.10.22
MA0140.10.00712
MA0141.10.0133
MA0142.10.0723
MA0143.10.774
MA0144.10.863
MA0145.10.479
MA0146.10.671
MA0147.10.0331
MA0148.10.0805
MA0149.10.268
MA0150.10.104
MA0152.10.0998
MA0153.10.861
MA0154.10.0758
MA0155.10.325
MA0156.10.248
MA0157.10.0471
MA0159.10.316
MA0160.10.00276
MA0162.10.34
MA0163.10.478
MA0164.10.449
MA0258.10.0489
MA0259.10.793



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: CNhs12404

Novel motifP-value
10.126
100.714
1000.709
1010.53
1020.164
1030.0885
1040.519
1050.5
1060.00716
1070.166
1080.632
1090.0874
110.141
1100.865
1110.0374
1120.453
1130.0235
1140.526
1150.387
1160.945
1170.834
1180.796
1190.29
120.826
1200.497
1210.786
1220.0323
1230.00968
1240.0587
1250.584
1260.211
1270.432
1280.0251
1290.274
130.611
1300.729
1310.335
1320.784
1330.912
1340.793
1350.766
1360.15
1370.527
1380.566
1390.103
140.602
1400.652
1410.403
1420.813
1430.0852
1440.962
1450.952
1460.0688
1470.229
1480.0161
1490.529
150.0256
1500.753
1510.047
1520.31
1530.962
1540.555
1550.0156
1560.783
1570.646
1580.455
1590.169
160.449
1600.29
1610.126
1620.888
1630.856
1640.728
1650.337
1660.0412
1670.508
1680.801
1690.502
170.68
180.8
190.914
20.525
200.875
210.24
220.731
230.797
240.335
250.153
260.909
270.269
280.746
290.815
30.563
300.69
310.466
325.79542e-4
330.569
340.609
350.656
360.0439
370.748
380.297
390.815
40.777
400.0209
410.207
420.337
430.235
440.271
450.226
460.352
470.159
480.358
490.142
50.552
500.776
510.414
520.409
530.31
540.394
550.765
560.337
570.61
580.14
590.258
60.811
600.0684
610.427
620.127
630.395
640.216
650.318
660.382
670.826
680.787
690.359
70.082
700.0196
710.625
720.409
730.53
740.0575
750.652
760.9
770.792
780.0803
790.0457
80.0611
800.216
810.438
820.428
830.0501
840.279
850.193
860.745
870.0895
880.605
890.567
90.694
900.192
910.917
920.419
930.442
940.214
950.379
960.977
970.839
980.035
990.212



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: CNhs12404


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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