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FF:11686-122I3: 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 17:22, 29 March 2012


Name:Cardiac Myocyte, donor3
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 number6755
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-0.204
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-lymphoma0.1
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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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: CNhs12571

Jaspar motifP-value
MA0002.20.121
MA0003.10.484
MA0004.10.0411
MA0006.10.196
MA0007.10.0432
MA0009.10.504
MA0014.10.739
MA0017.10.948
MA0018.24.32127e-5
MA0019.10.937
MA0024.10.879
MA0025.10.363
MA0027.10.928
MA0028.10.061
MA0029.10.354
MA0030.10.172
MA0031.10.268
MA0035.20.00459
MA0038.10.769
MA0039.20.406
MA0040.10.319
MA0041.10.3
MA0042.10.258
MA0043.10.102
MA0046.10.92
MA0047.20.81
MA0048.10.627
MA0050.14.30599e-4
MA0051.10.794
MA0052.10.613
MA0055.10.654
MA0057.10.317
MA0058.10.00207
MA0059.10.453
MA0060.10.0873
MA0061.10.0837
MA0062.21.2285e-7
MA0065.20.476
MA0066.10.326
MA0067.10.00461
MA0068.10.731
MA0069.10.913
MA0070.10.682
MA0071.10.606
MA0072.10.965
MA0073.10.992
MA0074.10.879
MA0076.10.00139
MA0077.10.39
MA0078.10.108
MA0079.20.914
MA0080.28.16256e-7
MA0081.10.0574
MA0083.10.00676
MA0084.10.128
MA0087.10.174
MA0088.10.647
MA0090.12.61168e-7
MA0091.10.0903
MA0092.10.00975
MA0093.10.0419
MA0099.20.00488
MA0100.10.533
MA0101.10.241
MA0102.20.471
MA0103.10.00179
MA0104.20.128
MA0105.10.0795
MA0106.10.593
MA0107.10.235
MA0108.24.35098e-12
MA0111.10.333
MA0112.20.228
MA0113.10.0375
MA0114.10.718
MA0115.10.0598
MA0116.10.966
MA0117.10.345
MA0119.10.119
MA0122.10.529
MA0124.10.226
MA0125.10.648
MA0131.10.432
MA0135.10.255
MA0136.12.30798e-8
MA0137.20.33
MA0138.20.316
MA0139.10.41
MA0140.19.19531e-4
MA0141.10.255
MA0142.10.355
MA0143.10.467
MA0144.10.175
MA0145.10.192
MA0146.10.696
MA0147.10.242
MA0148.10.847
MA0149.10.556
MA0150.10.0285
MA0152.10.0246
MA0153.10.712
MA0154.10.865
MA0155.10.537
MA0156.15.40785e-5
MA0157.10.705
MA0159.10.69
MA0160.10.77
MA0162.10.151
MA0163.10.836
MA0164.10.173
MA0258.10.825
MA0259.10.366



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: CNhs12571

Novel motifP-value
10.584
100.00917
1000.859
1010.751
1020.165
1030.433
1040.298
1050.596
1060.4
1070.0433
1080.622
1090.855
110.887
1100.949
1110.0378
1120.467
1130.0782
1140.406
1150.815
1160.264
1170.0122
1180.801
1190.682
120.693
1200.59
1210.777
1220.964
1232.43847e-4
1240.985
1250.519
1260.859
1270.775
1280.304
1290.722
130.584
1300.0397
1310.183
1320.343
1330.933
1340.118
1350.138
1360.695
1370.162
1380.144
1390.0691
140.254
1400.267
1410.876
1420.872
1430.623
1440.769
1450.899
1460.0945
1470.437
1480.43
1490.00471
150.963
1500.15
1510.596
1520.128
1530.651
1540.0839
1550.0183
1560.806
1570.533
1587.41707e-4
1590.296
160.175
1600.0982
1610.854
1620.933
1630.448
1640.94
1650.0523
1660.116
1670.092
1680.461
1690.148
170.932
180.24
190.0857
20.24
200.329
210.693
220.383
230.587
240.793
250.207
260.75
270.655
280.199
290.603
30.837
300.114
310.419
321.67756e-9
330.505
340.312
350.208
360.468
370.848
380.527
390.124
40.649
400.615
410.831
420.699
430.679
440.943
450.348
460.839
470.662
480.977
490.725
50.424
500.424
510.873
520.624
530.373
540.991
550.465
560.811
570.553
580.264
590.37
60.773
600.651
610.681
620.436
630.624
640.742
650.811
660.347
670.562
680.842
690.957
70.871
700.274
710.324
720.844
730.277
740.665
750.471
760.108
770.102
780.573
790.196
80.225
800.399
810.363
820.223
830.0685
840.293
850.182
860.27
870.0812
880.482
890.135
90.711
900.716
910.861
920.493
930.534
940.849
950.883
960.51
970.398
980.15
990.00419



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: CNhs12571


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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