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FF:11554-120C6: 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 walker warburg, 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
age1 month old neonate
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-0.0807
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-lymphoma0.283
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs11352

Jaspar motifP-value
MA0002.20.227
MA0003.10.381
MA0004.10.0413
MA0006.10.0851
MA0007.10.985
MA0009.10.318
MA0014.10.773
MA0017.10.352
MA0018.23.44188e-4
MA0019.10.47
MA0024.10.168
MA0025.10.00832
MA0027.10.32
MA0028.10.685
MA0029.10.247
MA0030.10.0475
MA0031.10.0306
MA0035.20.444
MA0038.10.203
MA0039.20.732
MA0040.10.974
MA0041.10.664
MA0042.10.767
MA0043.12.80858e-5
MA0046.10.368
MA0047.20.159
MA0048.10.0224
MA0050.18.37969e-4
MA0051.10.0151
MA0052.10.203
MA0055.10.032
MA0057.10.0778
MA0058.10.00631
MA0059.10.792
MA0060.10.278
MA0061.10.105
MA0062.20.0591
MA0065.20.679
MA0066.10.272
MA0067.12.59093e-4
MA0068.10.546
MA0069.10.172
MA0070.10.275
MA0071.10.685
MA0072.10.876
MA0073.10.892
MA0074.10.741
MA0076.10.886
MA0077.10.916
MA0078.10.478
MA0079.20.328
MA0080.22.15071e-8
MA0081.10.00252
MA0083.11.09203e-6
MA0084.10.246
MA0087.10.8
MA0088.10.103
MA0090.12.93524e-5
MA0091.10.217
MA0092.10.0466
MA0093.10.0649
MA0099.20.0212
MA0100.10.491
MA0101.10.00273
MA0102.20.0161
MA0103.19.05919e-5
MA0104.20.0295
MA0105.10.826
MA0106.10.0273
MA0107.10.0025
MA0108.21.90973e-5
MA0111.10.0538
MA0112.20.0271
MA0113.10.283
MA0114.10.0893
MA0115.10.339
MA0116.10.473
MA0117.10.718
MA0119.10.438
MA0122.10.278
MA0124.10.378
MA0125.10.493
MA0131.10.581
MA0135.10.464
MA0136.11.64909e-6
MA0137.20.643
MA0138.20.845
MA0139.10.548
MA0140.10.537
MA0141.10.552
MA0142.10.179
MA0143.10.602
MA0144.10.764
MA0145.10.398
MA0146.10.571
MA0147.10.123
MA0148.10.181
MA0149.10.962
MA0150.10.472
MA0152.10.0333
MA0153.10.594
MA0154.10.369
MA0155.10.587
MA0156.10.00183
MA0157.10.161
MA0159.10.53
MA0160.10.0634
MA0162.10.0461
MA0163.10.125
MA0164.10.864
MA0258.10.849
MA0259.10.983



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: CNhs11352

Novel motifP-value
10.314
100.385
1000.994
1010.459
1020.16
1030.952
1040.922
1050.938
1060.79
1070.45
1080.818
1090.299
110.691
1100.277
1110.341
1120.984
1130.0337
1140.784
1150.583
1160.171
1170.416
1180.745
1190.681
120.851
1200.744
1210.323
1220.775
1231.63445e-5
1240.837
1250.709
1260.398
1270.896
1280.997
1290.962
130.775
1300.0446
1310.46
1320.452
1330.442
1340.28
1350.229
1360.291
1370.26
1380.21
1390.0156
140.274
1400.212
1410.0391
1420.899
1430.583
1440.9
1450.48
1460.888
1470.0974
1480.0844
1490.0842
150.251
1500.362
1510.939
1520.053
1530.868
1540.477
1550.0118
1560.765
1570.0475
1580.00556
1590.522
160.187
1600.303
1610.353
1620.396
1630.866
1640.412
1650.228
1660.0686
1670.186
1680.733
1690.0664
170.714
180.121
190.0269
20.345
200.182
210.162
220.215
230.612
240.975
250.856
260.72
270.71
280.232
290.747
30.98
300.035
310.945
322.1789e-5
330.999
340.66
350.355
360.074
370.229
380.613
390.477
40.495
400.889
410.68
420.951
430.924
440.954
450.437
460.616
470.882
480.843
490.463
50.737
500.262
510.997
520.899
530.381
540.681
550.866
560.93
570.665
580.323
590.0952
60.905
600.562
610.242
620.779
630.559
640.885
650.695
660.224
670.859
680.844
690.434
70.626
700.0388
710.474
720.982
730.0575
740.365
750.715
760.128
770.0128
780.125
790.0659
80.607
800.965
810.882
820.85
830.192
840.494
850.418
860.801
870.178
880.416
890.0758
90.429
900.0564
910.822
920.977
930.183
940.562
950.194
960.64
970.832
980.288
998.93986e-4



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: CNhs11352


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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