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FF:10051-101G6: 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 16:51, 29 March 2012


Name:heart, adult, diseased, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueheart
dev stage92 years old adult
sexfemale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyClontech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number3040792
catalog numberCat:636581
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-penis0.706
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-0.492
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: CNhs11758

Jaspar motifP-value
MA0002.20.22
MA0003.10.0164
MA0004.10.0295
MA0006.10.213
MA0007.10.245
MA0009.10.0858
MA0014.10.536
MA0017.10.0473
MA0018.20.108
MA0019.10.065
MA0024.10.00284
MA0025.10.113
MA0027.10.894
MA0028.18.08583e-7
MA0029.10.252
MA0030.10.971
MA0031.10.936
MA0035.23.47891e-4
MA0038.19.1397e-4
MA0039.20.2
MA0040.10.936
MA0041.10.0352
MA0042.10.278
MA0043.10.00394
MA0046.10.494
MA0047.20.693
MA0048.10.0139
MA0050.13.31254e-4
MA0051.10.00312
MA0052.11.09753e-36
MA0055.10.0337
MA0057.10.21
MA0058.10.00711
MA0059.10.0341
MA0060.11.08399e-4
MA0061.10.0239
MA0062.29.82861e-12
MA0065.20.00267
MA0066.10.102
MA0067.10.204
MA0068.10.967
MA0069.10.805
MA0070.10.277
MA0071.10.00102
MA0072.10.423
MA0073.10.814
MA0074.10.41
MA0076.12.34951e-7
MA0077.10.615
MA0078.10.521
MA0079.20.23
MA0080.25.75972e-7
MA0081.10.0164
MA0083.10.00529
MA0084.10.756
MA0087.10.794
MA0088.10.179
MA0090.10.0583
MA0091.10.0508
MA0092.10.0989
MA0093.10.0222
MA0099.29.36373e-12
MA0100.10.0153
MA0101.10.053
MA0102.20.00567
MA0103.10.274
MA0104.28.29454e-4
MA0105.10.0532
MA0106.10.321
MA0107.10.0405
MA0108.22.34734e-10
MA0111.10.591
MA0112.25.2243e-5
MA0113.15.85979e-4
MA0114.10.0993
MA0115.10.00114
MA0116.10.856
MA0117.10.215
MA0119.10.151
MA0122.10.13
MA0124.10.76
MA0125.10.305
MA0131.10.0322
MA0135.10.0957
MA0136.11.79695e-11
MA0137.20.337
MA0138.20.0836
MA0139.10.984
MA0140.10.309
MA0141.14.76071e-10
MA0142.10.0601
MA0143.10.358
MA0144.10.499
MA0145.10.0329
MA0146.10.151
MA0147.10.00239
MA0148.10.69
MA0149.10.52
MA0150.10.0535
MA0152.10.745
MA0153.10.669
MA0154.10.177
MA0155.10.028
MA0156.14.75762e-10
MA0157.10.797
MA0159.16.61573e-4
MA0160.11.36062e-5
MA0162.10.214
MA0163.10.394
MA0164.10.999
MA0258.18.88573e-5
MA0259.10.0619



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: CNhs11758

Novel motifP-value
10.474
100.273
1000.963
1010.425
1020.835
1030.82
1040.544
1050.335
1060.0843
1070.0321
1080.272
1090.475
110.369
1100.705
1110.99
1120.0597
1130.84
1140.214
1150.209
1160.334
1170.0789
1180.276
1190.0587
120.975
1200.187
1210.868
1220.195
1230.268
1240.866
1250.985
1260.686
1270.99
1280.0799
1290.687
130.654
1300.791
1310.0953
1320.037
1330.245
1340.164
1350.095
1360.516
1370.988
1380.716
1390.0483
140.288
1400.111
1410.406
1420.53
1430.374
1440.489
1450.865
1460.408
1470.0184
1480.695
1490.00217
150.978
1500.801
1510.319
1520.212
1530.518
1540.973
1550.66
1560.173
1570.316
1580.33
1590.377
160.513
1600.164
1610.783
1620.983
1630.373
1640.265
1650.305
1660.0266
1670.151
1680.148
1690.011
170.377
180.573
190.0362
20.0422
200.0387
210.312
220.0618
230.0443
240.186
250.985
260.83
270.18
280.69
290.221
30.846
300.0929
310.524
320.338
330.646
340.113
350.539
360.231
370.545
380.667
390.106
40.655
400.628
410.683
420.473
430.55
440.00155
450.14
460.45
470.772
480.977
490.539
50.779
500.861
510.786
520.13
530.952
540.421
550.372
560.902
570.843
580.878
590.0848
60.824
600.24
610.434
620.378
630.528
640.627
650.063
660.0207
670.746
680.626
690.358
70.828
700.827
710.716
720.83
730.4
740.0465
750.476
760.132
770.0152
780.424
790.0242
80.453
800.873
810.738
820.127
830.409
840.466
850.00194
860.919
870.333
880.956
890.0439
90.426
900.0674
910.091
920.155
930.865
940.0511
950.546
960.451
970.894
980.0772
990.0387



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: CNhs11758


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

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0001009 (circulatory system)
0001062 (anatomical entity)
0007023 (adult organism)
0007100 (primary circulatory organ)

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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