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FF:11754-123G8: 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 17:18, 29 March 2012


Name:mesenchymal precursor cell - cardiac, 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 typemesenchymal precursor cell
cell lineNA
companyNA
collaborationClaudio Schneider LNCIB
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
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
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-lymphoma0.148
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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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: CNhs12370

Jaspar motifP-value
MA0002.20.0652
MA0003.10.913
MA0004.10.285
MA0006.10.872
MA0007.10.771
MA0009.10.318
MA0014.10.281
MA0017.10.104
MA0018.20.0553
MA0019.10.725
MA0024.10.242
MA0025.10.109
MA0027.10.897
MA0028.10.0948
MA0029.10.712
MA0030.10.16
MA0031.10.0191
MA0035.20.0215
MA0038.10.95
MA0039.20.00909
MA0040.10.793
MA0041.10.575
MA0042.10.849
MA0043.10.269
MA0046.10.18
MA0047.20.871
MA0048.10.0375
MA0050.10.00166
MA0051.10.0648
MA0052.10.0534
MA0055.10.0597
MA0057.10.642
MA0058.10.478
MA0059.10.525
MA0060.10.0165
MA0061.10.516
MA0062.20.267
MA0065.20.0149
MA0066.10.828
MA0067.10.644
MA0068.10.522
MA0069.10.173
MA0070.10.566
MA0071.10.71
MA0072.10.37
MA0073.10.598
MA0074.10.123
MA0076.10.199
MA0077.10.403
MA0078.10.331
MA0079.20.353
MA0080.23.83363e-7
MA0081.10.0516
MA0083.10.0339
MA0084.10.0572
MA0087.10.66
MA0088.10.311
MA0090.10.00983
MA0091.10.38
MA0092.10.416
MA0093.10.602
MA0099.22.45678e-8
MA0100.10.529
MA0101.10.849
MA0102.20.606
MA0103.13.9314e-6
MA0104.20.452
MA0105.10.108
MA0106.10.235
MA0107.10.785
MA0108.20.141
MA0111.10.257
MA0112.20.176
MA0113.10.582
MA0114.10.0423
MA0115.10.294
MA0116.10.107
MA0117.10.829
MA0119.10.493
MA0122.10.467
MA0124.10.119
MA0125.10.135
MA0131.10.788
MA0135.10.151
MA0136.12.69581e-5
MA0137.20.238
MA0138.20.48
MA0139.10.979
MA0140.10.316
MA0141.10.779
MA0142.10.178
MA0143.10.687
MA0144.10.246
MA0145.10.68
MA0146.10.266
MA0147.10.724
MA0148.10.985
MA0149.10.738
MA0150.10.173
MA0152.13.05152e-4
MA0153.10.497
MA0154.10.286
MA0155.10.962
MA0156.10.00581
MA0157.10.107
MA0159.10.4
MA0160.10.159
MA0162.10.135
MA0163.10.00595
MA0164.10.75
MA0258.10.638
MA0259.10.588



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: CNhs12370

Novel motifP-value
10.958
100.364
1000.285
1010.314
1020.216
1030.377
1040.654
1050.0468
1060.891
1070.704
1080.662
1090.807
110.602
1100.0591
1110.0998
1120.77
1130.00349
1140.884
1150.224
1160.0277
1170.37
1180.309
1190.596
120.388
1200.245
1210.812
1220.014
1231.01839e-4
1240.153
1250.87
1260.996
1270.628
1280.953
1290.91
130.927
1300.236
1310.348
1320.696
1330.864
1340.419
1350.214
1360.693
1370.59
1380.733
1390.573
140.195
1400.24
1410.581
1420.376
1430.458
1440.49
1450.994
1460.92
1470.16
1480.663
1490.346
150.802
1500.104
1510.411
1520.349
1530.998
1540.459
1550.00844
1560.307
1570.597
1580.005
1590.138
160.0672
1600.936
1610.393
1620.994
1630.75
1640.368
1650.189
1660.249
1670.83
1680.751
1690.093
170.922
180.249
190.0526
20.481
200.459
210.432
220.489
230.412
240.616
250.176
260.334
270.945
280.339
290.443
30.658
300.449
310.988
322.05675e-10
330.752
340.442
350.864
360.0982
370.243
380.524
390.125
40.209
400.12
410.572
420.843
430.824
440.458
450.745
460.712
470.606
480.832
490.073
50.888
500.481
510.969
520.489
530.0161
540.891
550.447
560.412
570.489
580.2
590.348
60.199
600.721
610.837
620.822
630.914
640.679
650.539
660.515
670.488
680.869
690.259
70.404
700.371
710.469
720.542
730.076
740.0926
750.671
760.716
770.012
780.0455
790.0115
80.35
800.988
810.962
820.567
830.943
840.725
850.793
860.168
870.0574
880.428
890.111
90.524
900.651
910.824
920.509
930.841
940.442
950.323
960.938
970.297
980.0522
990.0669



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: CNhs12370


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)
0000011 (migratory trunk neural crest cell)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000133 (neurectodermal cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000333 (migratory neural crest cell)
0000548 (animal cell)
0000569 (cardiac mesenchymal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002494 (cardiocyte)

UBERON: Anatomy
0000025 (tube)
0000061 (anatomical structure)
0000062 (organ)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000948 (heart)
0001009 (circulatory system)
0001048 (primordium)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002384 (connective tissue)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003084 (heart primordium)
0003914 (epithelial tube)
0004120 (mesoderm-derived structure)
0004140 (primary heart field)
0004141 (heart tube)
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)

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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