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FF:11559-120D2: 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 17:01, 29 March 2012


Name:Fibroblast - skin spinal muscular atrophy, donor3
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
age7 month 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-0.0952
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-lymphoma0.346
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs11912

Jaspar motifP-value
MA0002.20.409
MA0003.10.994
MA0004.16.72758e-4
MA0006.10.0747
MA0007.10.306
MA0009.10.314
MA0014.10.612
MA0017.10.0912
MA0018.25.45172e-5
MA0019.10.0863
MA0024.10.517
MA0025.10.0289
MA0027.10.9
MA0028.10.266
MA0029.10.332
MA0030.10.0736
MA0031.10.1
MA0035.20.0128
MA0038.10.298
MA0039.20.0669
MA0040.10.418
MA0041.10.64
MA0042.10.965
MA0043.13.09981e-5
MA0046.10.742
MA0047.20.231
MA0048.10.00239
MA0050.14.31937e-7
MA0051.10.00102
MA0052.10.186
MA0055.10.081
MA0057.10.425
MA0058.13.40705e-4
MA0059.10.0913
MA0060.10.891
MA0061.10.00628
MA0062.20.163
MA0065.20.0326
MA0066.10.467
MA0067.10.0388
MA0068.10.873
MA0069.10.0329
MA0070.10.751
MA0071.10.622
MA0072.10.736
MA0073.10.884
MA0074.10.805
MA0076.10.271
MA0077.10.638
MA0078.10.307
MA0079.20.766
MA0080.26.77635e-9
MA0081.10.00554
MA0083.10.00183
MA0084.10.398
MA0087.10.669
MA0088.10.444
MA0090.11.11241e-4
MA0091.10.82
MA0092.10.358
MA0093.10.00487
MA0099.20.143
MA0100.10.223
MA0101.17.38076e-6
MA0102.20.0048
MA0103.13.10238e-6
MA0104.23.71921e-5
MA0105.10.399
MA0106.10.0226
MA0107.19.41817e-6
MA0108.20.0839
MA0111.10.228
MA0112.20.247
MA0113.10.977
MA0114.10.0144
MA0115.10.155
MA0116.10.853
MA0117.10.622
MA0119.10.799
MA0122.10.448
MA0124.10.568
MA0125.10.696
MA0131.10.748
MA0135.10.991
MA0136.17.0904e-6
MA0137.20.283
MA0138.20.476
MA0139.10.487
MA0140.10.0986
MA0141.10.166
MA0142.10.112
MA0143.10.786
MA0144.10.299
MA0145.10.492
MA0146.10.494
MA0147.10.00109
MA0148.10.313
MA0149.10.758
MA0150.10.159
MA0152.10.136
MA0153.10.899
MA0154.10.994
MA0155.10.715
MA0156.10.0174
MA0157.10.328
MA0159.10.596
MA0160.10.0235
MA0162.10.0532
MA0163.10.152
MA0164.10.74
MA0258.10.297
MA0259.10.275



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: CNhs11912

Novel motifP-value
10.431
100.857
1000.58
1010.292
1020.171
1030.626
1040.953
1050.684
1060.119
1070.986
1080.826
1090.698
110.696
1100.663
1110.507
1120.949
1130.00199
1140.907
1150.435
1160.28
1170.391
1180.637
1190.192
120.776
1200.638
1210.591
1220.217
1233.90308e-5
1240.316
1250.413
1260.405
1270.828
1280.292
1290.506
130.689
1300.0504
1310.506
1320.68
1330.496
1340.208
1350.543
1360.16
1370.915
1380.259
1390.0331
140.248
1400.145
1410.038
1420.676
1430.917
1440.559
1450.755
1460.949
1470.264
1480.0209
1490.0346
150.465
1500.502
1510.33
1520.146
1530.614
1540.412
1550.00956
1560.659
1570.149
1580.00251
1590.171
160.487
1600.851
1610.0656
1620.726
1630.344
1640.341
1650.16
1660.0607
1670.496
1680.31
1690.226
170.966
180.239
190.0258
20.403
200.354
210.137
220.431
230.975
240.985
250.604
260.897
270.942
280.522
290.759
30.805
300.227
310.964
327.88631e-6
330.353
340.968
350.386
360.0722
370.43
380.56
390.401
40.802
400.26
410.465
420.729
430.652
440.985
450.9
460.856
470.72
480.645
490.105
50.699
500.725
510.615
520.709
530.259
540.981
550.382
560.749
570.514
580.202
590.294
60.575
600.296
610.265
620.456
630.719
640.554
650.861
660.431
670.623
680.712
690.762
70.131
700.139
710.959
720.227
730.138
740.105
750.556
760.457
770.0656
780.233
790.17
80.993
800.596
810.49
820.922
830.2
840.278
850.685
860.4
870.188
880.741
890.36
90.83
900.685
910.771
920.805
930.32
940.974
950.944
960.922
970.581
980.154
990.0669



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: CNhs11912


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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