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FF:11553-120C5: 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 16:46, 29 March 2012


Name:Fibroblast - skin normal, 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
sexM
age25 year old
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-0.114
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-0.169
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: CNhs11351

Jaspar motifP-value
MA0002.20.869
MA0003.10.359
MA0004.10.00671
MA0006.10.103
MA0007.10.715
MA0009.10.215
MA0014.10.459
MA0017.10.494
MA0018.21.17856e-6
MA0019.10.554
MA0024.11.16242e-7
MA0025.10.0335
MA0027.10.529
MA0028.10.249
MA0029.10.686
MA0030.10.117
MA0031.10.207
MA0035.20.00657
MA0038.10.0426
MA0039.20.172
MA0040.10.276
MA0041.10.495
MA0042.10.602
MA0043.11.03909e-5
MA0046.10.674
MA0047.20.643
MA0048.10.187
MA0050.10.18
MA0051.10.5
MA0052.10.787
MA0055.10.952
MA0057.10.113
MA0058.10.00161
MA0059.10.118
MA0060.17.8537e-9
MA0061.10.0547
MA0062.22.00716e-4
MA0065.20.219
MA0066.10.34
MA0067.10.00191
MA0068.10.976
MA0069.10.0222
MA0070.10.566
MA0071.10.513
MA0072.10.598
MA0073.10.992
MA0074.10.913
MA0076.10.192
MA0077.10.268
MA0078.10.685
MA0079.20.994
MA0080.22.51023e-7
MA0081.10.0173
MA0083.10.0262
MA0084.10.443
MA0087.10.867
MA0088.10.898
MA0090.15.67698e-6
MA0091.10.151
MA0092.10.104
MA0093.10.0158
MA0099.20.293
MA0100.10.237
MA0101.14.01735e-4
MA0102.20.0692
MA0103.12.20978e-4
MA0104.28.12367e-4
MA0105.10.192
MA0106.10.0158
MA0107.10.00226
MA0108.20.0938
MA0111.10.099
MA0112.20.0315
MA0113.10.93
MA0114.10.414
MA0115.10.0768
MA0116.10.893
MA0117.10.305
MA0119.11
MA0122.10.686
MA0124.10.531
MA0125.10.322
MA0131.10.393
MA0135.10.828
MA0136.11.035e-8
MA0137.20.528
MA0138.20.347
MA0139.10.612
MA0140.10.0657
MA0141.10.395
MA0142.10.0281
MA0143.10.998
MA0144.10.898
MA0145.10.309
MA0146.10.633
MA0147.10.00536
MA0148.10.641
MA0149.10.321
MA0150.10.0573
MA0152.10.0349
MA0153.10.334
MA0154.10.505
MA0155.10.414
MA0156.11.21863e-4
MA0157.10.622
MA0159.10.83
MA0160.10.107
MA0162.10.0856
MA0163.10.197
MA0164.10.613
MA0258.10.969
MA0259.10.143



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: CNhs11351

Novel motifP-value
10.385
100.472
1000.581
1010.594
1020.0342
1030.655
1040.719
1050.615
1060.935
1070.563
1080.96
1090.474
110.74
1100.891
1110.535
1120.697
1137.25794e-4
1140.569
1150.315
1160.109
1170.268
1180.618
1190.523
120.586
1200.896
1210.712
1220.651
1236.87201e-5
1240.629
1250.826
1260.883
1270.74
1280.998
1290.431
130.361
1300.113
1310.786
1320.222
1330.537
1340.513
1350.135
1360.0712
1370.406
1380.409
1390.743
140.37
1400.35
1410.193
1420.81
1430.854
1440.754
1450.951
1460.984
1470.0511
1480.514
1490.00511
150.366
1500.341
1510.698
1520.0568
1530.2
1540.882
1550.00862
1560.795
1570.236
1580.00668
1590.707
160.105
1600.579
1610.34
1620.775
1630.804
1640.687
1650.532
1660.0488
1670.279
1680.301
1690.0551
170.905
180.144
190.0118
20.215
200.226
210.0464
220.261
230.302
240.358
250.3
260.515
270.595
280.283
290.716
30.802
300.131
310.776
322.26669e-11
330.433
340.834
350.556
360.0489
370.213
380.492
390.167
40.663
400.235
410.669
420.387
430.734
440.701
450.677
460.897
470.583
480.729
490.325
50.488
500.432
510.667
520.88
530.177
540.796
550.204
560.791
570.837
580.25
590.158
60.986
600.629
610.26
620.649
630.724
640.538
650.8
660.337
670.937
680.744
690.989
70.169
700.674
710.794
720.82
730.0577
740.48
750.319
760.44
770.0575
780.0926
790.0727
80.77
800.955
810.749
820.122
830.108
840.207
850.86
860.518
870.378
880.636
890.113
90.498
900.245
910.713
920.231
930.701
940.789
950.905
960.879
970.592
980.425
990.0107



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: CNhs11351


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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