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FF:11605-120I3: 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 17:17, 29 March 2012


Name:Cardiac Myocyte, donor2
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 stageNA
sexNA
ageNA
cell typecardiac muscle cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberSC6205
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-0.0934
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-lymphoma0.0363
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: CNhs12350

Jaspar motifP-value
MA0002.20.304
MA0003.10.288
MA0004.10.324
MA0006.10.057
MA0007.10.0965
MA0009.10.568
MA0014.10.828
MA0017.10.224
MA0018.21.46322e-5
MA0019.10.495
MA0024.10.0445
MA0025.16.5233e-4
MA0027.10.508
MA0028.10.366
MA0029.10.53
MA0030.10.767
MA0031.10.818
MA0035.25.39776e-4
MA0038.10.809
MA0039.20.512
MA0040.10.446
MA0041.10.255
MA0042.10.629
MA0043.14.95109e-4
MA0046.10.37
MA0047.20.96
MA0048.10.712
MA0050.10.252
MA0051.10.3
MA0052.10.0351
MA0055.10.535
MA0057.10.429
MA0058.10.063
MA0059.10.768
MA0060.10.286
MA0061.10.698
MA0062.21.72894e-4
MA0065.20.062
MA0066.10.0296
MA0067.10.0369
MA0068.10.292
MA0069.10.713
MA0070.10.422
MA0071.10.349
MA0072.10.785
MA0073.10.917
MA0074.10.181
MA0076.10.0331
MA0077.10.68
MA0078.10.116
MA0079.20.223
MA0080.21.38207e-5
MA0081.10.0333
MA0083.10.00338
MA0084.10.144
MA0087.10.155
MA0088.10.565
MA0090.10.0119
MA0091.10.142
MA0092.10.291
MA0093.10.258
MA0099.20.0733
MA0100.10.216
MA0101.10.51
MA0102.20.787
MA0103.10.00422
MA0104.20.331
MA0105.10.0641
MA0106.10.389
MA0107.10.329
MA0108.20.00278
MA0111.10.985
MA0112.20.00251
MA0113.10.0235
MA0114.10.383
MA0115.10.582
MA0116.10.0268
MA0117.10.521
MA0119.10.237
MA0122.10.8
MA0124.10.885
MA0125.10.811
MA0131.10.0568
MA0135.10.139
MA0136.11.31225e-7
MA0137.20.00717
MA0138.20.419
MA0139.10.547
MA0140.10.014
MA0141.10.0312
MA0142.10.775
MA0143.10.655
MA0144.10.015
MA0145.10.241
MA0146.10.276
MA0147.10.377
MA0148.10.682
MA0149.10.555
MA0150.10.151
MA0152.10.0223
MA0153.10.918
MA0154.10.0506
MA0155.10.137
MA0156.14.04058e-4
MA0157.10.971
MA0159.10.00684
MA0160.10.407
MA0162.10.194
MA0163.10.00505
MA0164.10.279
MA0258.10.0709
MA0259.10.292



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: CNhs12350

Novel motifP-value
10.4
100.862
1000.748
1010.604
1020.175
1030.162
1040.264
1050.811
1060.0359
1070.00472
1080.316
1090.778
110.127
1100.1
1110.0841
1120.446
1130.0873
1140.603
1150.312
1160.0526
1170.334
1180.794
1190.941
120.297
1200.0828
1210.182
1220.369
1230.00414
1240.375
1250.83
1260.443
1270.14
1280.00932
1290.919
130.799
1300.118
1310.795
1320.317
1330.383
1340.381
1350.434
1360.49
1370.481
1380.748
1390.538
140.678
1400.879
1410.39
1420.309
1430.364
1440.124
1450.283
1460.105
1470.242
1480.496
1490.0752
150.494
1500.217
1510.485
1520.185
1530.846
1540.389
1550.0343
1560.58
1570.699
1580.00543
1590.152
160.0782
1600.0626
1610.881
1620.311
1630.844
1640.375
1650.996
1660.105
1670.197
1680.644
1690.0582
170.845
180.281
190.0474
20.212
200.331
210.393
220.18
230.166
240.531
250.617
260.111
270.407
280.359
290.254
30.276
300.326
310.864
321.28563e-10
330.33
340.116
350.499
360.872
370.2
380.76
390.0352
40.163
400.893
410.605
420.702
430.166
440.0451
450.392
460.137
470.649
480.377
490.38
50.342
500.336
510.486
520.433
530.382
540.915
550.843
560.875
570.682
580.992
590.0415
60.855
600.766
610.591
620.364
630.379
640.444
650.167
660.739
670.905
680.93
690.298
70.898
700.491
710.0649
720.6
730.12
740.257
750.501
760.561
770.127
780.911
790.117
80.0369
800.718
810.671
820.295
830.43
840.72
850.00899
860.758
870.0259
880.536
890.144
90.224
900.976
910.457
920.477
930.306
940.59
950.413
960.744
970.822
980.362
990.00408



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: CNhs12350


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)
0000056 (myoblast)
0000183 (contractile cell)
0000187 (muscle cell)
0000211 (electrically active cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000355 (multi-potent skeletal muscle stem cell)
0000393 (electrically responsive cell)
0000513 (cardiac muscle myoblast)
0000548 (animal cell)
0000680 (muscle precursor cell)
0000723 (somatic stem cell)
0000737 (striated muscle cell)
0000746 (cardiac muscle cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002494 (cardiocyte)

UBERON: Anatomy
0000025 (tube)
0000061 (anatomical structure)
0000062 (organ)
0000119 (cell layer)
0000383 (musculature of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000948 (heart)
0001009 (circulatory system)
0001015 (musculature)
0001048 (primordium)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0002036 (striated muscle tissue)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002329 (somite)
0002385 (muscle tissue)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003081 (lateral plate mesoderm)
0003082 (myotome)
0003084 (heart primordium)
0003104 (mesenchyme)
0003914 (epithelial tube)
0004120 (mesoderm-derived structure)
0004140 (primary heart field)
0004141 (heart tube)
0004290 (dermomyotome)
0004291 (heart rudiment)
0004535 (cardiovascular system)
0004872 (splanchnic layer of lateral plate mesoderm)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005498 (primitive heart tube)
0007005 (cardiac mesoderm)
0007100 (primary circulatory organ)
0009142 (entire embryonic mesenchyme)

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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