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FF:11755-123G9: 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, donor4
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-penis0.0137
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-lymphoma0.322
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: CNhs12371

Jaspar motifP-value
MA0002.20.202
MA0003.10.723
MA0004.10.292
MA0006.10.456
MA0007.10.549
MA0009.10.341
MA0014.10.641
MA0017.10.513
MA0018.20.074
MA0019.10.302
MA0024.10.126
MA0025.10.196
MA0027.10.9
MA0028.10.00442
MA0029.10.701
MA0030.10.107
MA0031.10.0228
MA0035.20.0204
MA0038.10.47
MA0039.20.00991
MA0040.10.487
MA0041.10.517
MA0042.10.941
MA0043.10.259
MA0046.10.0633
MA0047.20.716
MA0048.10.113
MA0050.10.0169
MA0051.10.132
MA0052.10.641
MA0055.10.0208
MA0057.10.663
MA0058.10.234
MA0059.10.669
MA0060.10.00161
MA0061.10.428
MA0062.20.51
MA0065.20.154
MA0066.10.756
MA0067.10.133
MA0068.10.67
MA0069.10.441
MA0070.10.801
MA0071.10.136
MA0072.10.671
MA0073.10.53
MA0074.10.359
MA0076.10.0347
MA0077.10.619
MA0078.10.348
MA0079.20.137
MA0080.23.74578e-5
MA0081.10.366
MA0083.10.0596
MA0084.10.0496
MA0087.10.331
MA0088.10.636
MA0090.10.0178
MA0091.10.385
MA0092.10.442
MA0093.10.531
MA0099.22.03427e-9
MA0100.10.757
MA0101.10.0527
MA0102.20.558
MA0103.11.95124e-5
MA0104.20.293
MA0105.10.102
MA0106.10.333
MA0107.10.113
MA0108.20.00298
MA0111.10.138
MA0112.20.338
MA0113.10.911
MA0114.10.141
MA0115.10.376
MA0116.10.511
MA0117.10.681
MA0119.10.132
MA0122.10.698
MA0124.10.681
MA0125.10.282
MA0131.10.966
MA0135.10.104
MA0136.18.29483e-4
MA0137.20.163
MA0138.20.16
MA0139.10.842
MA0140.10.418
MA0141.10.76
MA0142.10.774
MA0143.10.819
MA0144.10.0506
MA0145.10.59
MA0146.10.0361
MA0147.10.623
MA0148.10.672
MA0149.10.812
MA0150.10.0199
MA0152.10.0022
MA0153.10.39
MA0154.10.511
MA0155.10.959
MA0156.10.615
MA0157.10.0254
MA0159.10.782
MA0160.10.275
MA0162.10.145
MA0163.10.0156
MA0164.10.886
MA0258.10.305
MA0259.10.362



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: CNhs12371

Novel motifP-value
10.754
100.246
1000.763
1010.501
1020.445
1030.121
1040.898
1050.153
1060.769
1070.361
1080.405
1090.637
110.651
1100.15
1110.196
1120.879
1130.00394
1140.768
1150.444
1160.0705
1170.336
1180.471
1190.956
120.583
1200.133
1210.924
1220.354
1231.3611e-4
1240.0635
1250.287
1260.55
1270.616
1280.945
1290.328
130.49
1300.208
1310.0696
1320.705
1330.632
1340.438
1350.45
1360.766
1370.985
1380.952
1390.297
140.2
1400.92
1410.92
1420.435
1430.191
1440.463
1450.761
1460.763
1470.0633
1480.483
1490.83
150.643
1500.0125
1510.154
1520.453
1530.479
1540.503
1550.00586
1560.345
1570.461
1580.0117
1590.0689
160.187
1600.797
1610.0295
1620.495
1630.289
1640.094
1650.61
1660.324
1670.532
1680.434
1690.418
170.912
180.119
190.284
20.958
200.844
210.943
220.987
230.211
240.498
250.159
260.47
270.463
280.483
290.0615
30.477
300.963
310.788
320.0018
330.273
340.649
350.625
360.492
370.11
380.438
390.311
40.271
400.33
410.923
420.972
430.677
440.505
450.574
460.547
470.94
480.707
490.0385
50.854
500.841
510.707
520.411
530.0162
540.753
550.389
560.207
570.974
580.17
590.96
60.289
600.576
610.474
620.559
630.996
640.533
650.991
660.643
670.609
680.766
690.352
70.321
700.138
710.591
720.95
730.0689
740.124
750.644
760.235
770.102
780.154
790.164
80.449
800.606
810.975
820.0932
830.891
840.787
850.435
860.351
870.0267
880.556
890.0684
90.612
900.244
910.596
920.852
930.511
940.907
950.134
960.821
970.418
980.111
990.106



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: CNhs12371


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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