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FF:14305-155C3: 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, donor3 (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
age7 month 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-penis0.261
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-lymphoma0.277
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs12398

Jaspar motifP-value
MA0002.20.0969
MA0003.10.48
MA0004.10.0276
MA0006.10.607
MA0007.10.156
MA0009.10.464
MA0014.10.373
MA0017.10.00408
MA0018.20.53
MA0019.10.491
MA0024.10.232
MA0025.10.0174
MA0027.10.844
MA0028.10.208
MA0029.10.802
MA0030.10.154
MA0031.10.0834
MA0035.28.05032e-5
MA0038.10.934
MA0039.20.023
MA0040.10.594
MA0041.10.797
MA0042.10.852
MA0043.10.122
MA0046.10.359
MA0047.20.844
MA0048.10.00683
MA0050.10.00112
MA0051.10.00315
MA0052.10.317
MA0055.10.6
MA0057.10.651
MA0058.10.00855
MA0059.10.0357
MA0060.10.239
MA0061.16.06367e-4
MA0062.20.0187
MA0065.20.00161
MA0066.10.756
MA0067.10.855
MA0068.10.575
MA0069.10.0129
MA0070.10.319
MA0071.10.201
MA0072.10.257
MA0073.10.71
MA0074.10.46
MA0076.10.722
MA0077.10.233
MA0078.10.627
MA0079.20.123
MA0080.21.35004e-8
MA0081.10.0377
MA0083.13.7531e-4
MA0084.10.639
MA0087.10.437
MA0088.10.208
MA0090.11.7326e-4
MA0091.10.855
MA0092.10.717
MA0093.10.0461
MA0099.20.941
MA0100.10.432
MA0101.19.23601e-5
MA0102.20.193
MA0103.17.02537e-6
MA0104.22.46938e-4
MA0105.10.0403
MA0106.10.216
MA0107.11.59764e-4
MA0108.20.106
MA0111.10.138
MA0112.20.538
MA0113.10.492
MA0114.10.00152
MA0115.10.0334
MA0116.10.502
MA0117.10.404
MA0119.10.726
MA0122.10.268
MA0124.10.0806
MA0125.10.149
MA0131.10.754
MA0135.10.484
MA0136.12.74773e-7
MA0137.20.111
MA0138.20.653
MA0139.10.408
MA0140.10.0123
MA0141.10.00466
MA0142.10.1
MA0143.10.996
MA0144.10.196
MA0145.10.925
MA0146.10.0688
MA0147.10.0044
MA0148.10.212
MA0149.10.152
MA0150.10.0932
MA0152.10.212
MA0153.10.991
MA0154.10.598
MA0155.10.724
MA0156.10.00384
MA0157.10.123
MA0159.10.176
MA0160.14.73799e-4
MA0162.10.0318
MA0163.10.537
MA0164.10.59
MA0258.10.374
MA0259.10.27



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: CNhs12398

Novel motifP-value
10.0768
100.376
1000.486
1010.309
1020.0758
1030.313
1040.929
1050.529
1060.126
1070.975
1080.919
1090.013
110.129
1100.624
1110.0703
1120.602
1130.0163
1140.322
1150.262
1160.779
1170.105
1180.414
1190.307
120.937
1200.754
1210.838
1220.0595
1230.00104
1240.063
1250.704
1260.233
1270.516
1280.188
1290.107
130.619
1300.991
1310.399
1320.623
1330.328
1340.923
1350.837
1360.131
1370.918
1380.533
1390.108
140.447
1400.608
1410.214
1420.984
1430.667
1440.719
1450.928
1460.142
1470.158
1480.11
1490.266
150.0534
1500.608
1510.131
1520.479
1530.648
1540.482
1550.0167
1560.589
1570.34
1580.108
1590.715
160.806
1600.257
1610.022
1620.581
1630.382
1640.91
1650.703
1660.00483
1670.314
1680.991
1690.853
170.719
180.759
190.257
20.897
200.418
210.502
220.825
230.801
240.37
250.126
260.896
270.488
280.688
290.958
30.445
300.569
310.667
328.05793e-7
330.215
340.611
350.515
360.0245
370.72
380.278
390.978
40.35
400.0466
410.78
420.286
430.451
440.373
450.492
460.499
470.128
480.332
490.0708
50.734
500.799
510.466
520.645
530.323
540.486
550.533
560.294
570.994
580.119
590.73
60.872
600.309
610.144
620.0841
630.565
640.207
650.473
660.43
670.813
680.866
690.676
70.0684
700.0748
710.804
720.271
730.448
740.323
750.0754
760.534
770.898
780.0126
790.149
80.181
800.551
810.38
820.725
830.0539
840.362
850.683
860.521
870.486
880.721
890.923
90.969
900.237
910.8
920.429
930.641
940.556
950.016
960.735
970.531
980.0486
990.521



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: CNhs12398


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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