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FF:11525-119I4: 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 17:16, 29 March 2012


Name:Cardiac Myocyte, 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 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-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-penis-0.0622
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-0.47
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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: CNhs12341

Jaspar motifP-value
MA0002.20.896
MA0003.10.959
MA0004.10.475
MA0006.10.509
MA0007.10.393
MA0009.10.229
MA0014.10.00273
MA0017.10.59
MA0018.21.03986e-5
MA0019.10.377
MA0024.11.46846e-4
MA0025.11.70051e-5
MA0027.10.827
MA0028.19.91381e-10
MA0029.10.0876
MA0030.10.573
MA0031.10.593
MA0035.20.232
MA0038.13.00513e-5
MA0039.28.14171e-4
MA0040.10.726
MA0041.10.537
MA0042.10.583
MA0043.15.18946e-4
MA0046.10.481
MA0047.20.517
MA0048.10.663
MA0050.10.335
MA0051.10.956
MA0052.10.537
MA0055.10.0108
MA0057.10.853
MA0058.10.183
MA0059.10.532
MA0060.15.36614e-10
MA0061.10.801
MA0062.23.61966e-21
MA0065.20.682
MA0066.10.247
MA0067.10.165
MA0068.10.845
MA0069.10.563
MA0070.10.393
MA0071.10.358
MA0072.10.541
MA0073.10.707
MA0074.10.2
MA0076.13.28961e-12
MA0077.10.252
MA0078.10.764
MA0079.20.239
MA0080.27.94155e-6
MA0081.18.09519e-4
MA0083.10.0169
MA0084.10.848
MA0087.10.992
MA0088.10.0447
MA0090.10.0142
MA0091.10.00132
MA0092.10.0723
MA0093.10.342
MA0099.20.0417
MA0100.10.116
MA0101.10.364
MA0102.20.581
MA0103.10.00739
MA0104.20.171
MA0105.10.0274
MA0106.10.172
MA0107.10.287
MA0108.20.874
MA0111.10.334
MA0112.24.83503e-4
MA0113.10.01
MA0114.10.766
MA0115.10.867
MA0116.10.167
MA0117.10.352
MA0119.10.0111
MA0122.10.738
MA0124.10.796
MA0125.10.536
MA0131.10.0334
MA0135.10.162
MA0136.12.39752e-13
MA0137.20.219
MA0138.20.259
MA0139.10.192
MA0140.10.34
MA0141.10.834
MA0142.10.253
MA0143.10.152
MA0144.10.0349
MA0145.10.0615
MA0146.10.713
MA0147.10.439
MA0148.10.113
MA0149.10.344
MA0150.10.538
MA0152.17.94852e-4
MA0153.10.027
MA0154.10.154
MA0155.10.379
MA0156.12.40531e-9
MA0157.10.29
MA0159.10.765
MA0160.10.96
MA0162.10.395
MA0163.10.169
MA0164.10.671
MA0258.10.132
MA0259.10.262



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: CNhs12341

Novel motifP-value
10.89
100.889
1000.584
1010.654
1020.145
1030.0584
1040.97
1050.79
1060.0122
1073.57899e-4
1080.477
1090.406
110.835
1100.753
1110.968
1120.176
1130.784
1140.124
1150.414
1160.722
1170.585
1180.363
1190.146
120.652
1200.908
1210.886
1220.185
1230.478
1240.378
1250.395
1260.595
1270.527
1287.27608e-4
1290.257
130.324
1300.567
1310.646
1320.716
1330.514
1340.463
1350.867
1360.0701
1370.741
1380.139
1390.0245
140.59
1400.00595
1410.633
1420.76
1430.493
1440.101
1450.288
1460.606
1470.105
1480.589
1490.0337
150.106
1500.358
1510.143
1520.848
1530.193
1540.894
1550.253
1560.678
1570.313
1580.113
1590.76
160.222
1600.0279
1610.619
1620.404
1630.492
1640.55
1650.78
1660.0257
1670.595
1680.219
1690.0712
170.852
180.17
190.0745
20.078
200.152
210.342
220.154
230.0016
240.277
250.333
260.174
270.376
280.498
290.816
30.518
300.494
310.338
326.53836e-6
330.537
340.238
350.236
360.0506
370.767
380.863
390.231
40.788
400.0112
410.925
420.748
430.199
440.15
450.298
460.0597
470.796
480.47
490.223
50.146
500.77
510.609
520.18
530.586
540.846
550.0277
560.509
570.621
580.496
590.126
60.745
600.164
610.604
620.14
630.339
640.6
650.178
660.207
670.652
680.974
690.699
70.984
700.02
710.136
720.478
730.468
740.53
750.989
760.718
770.268
780.699
790.163
80.0852
800.835
810.192
820.0445
830.572
840.463
850.00875
860.456
870.2
880.361
890.0635
90.392
900.0813
910.0166
920.00178
930.371
940.368
950.0405
960.61
970.226
980.399
990.195



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: CNhs12341


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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