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FF:11753-123G7: 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, 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 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-penis0.0342
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-0.184
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: CNhs12369

Jaspar motifP-value
MA0002.20.162
MA0003.10.436
MA0004.10.589
MA0006.10.661
MA0007.10.773
MA0009.10.231
MA0014.10.589
MA0017.10.347
MA0018.20.0892
MA0019.10.657
MA0024.11.77784e-4
MA0025.10.117
MA0027.10.811
MA0028.10.0395
MA0029.10.104
MA0030.10.0467
MA0031.10.0831
MA0035.20.448
MA0038.10.0199
MA0039.20.00452
MA0040.10.0732
MA0041.10.336
MA0042.10.45
MA0043.10.283
MA0046.10.115
MA0047.20.959
MA0048.10.104
MA0050.10.629
MA0051.10.537
MA0052.10.224
MA0055.10.356
MA0057.10.703
MA0058.10.406
MA0059.10.549
MA0060.17.38729e-9
MA0061.10.237
MA0062.29.59943e-7
MA0065.20.0557
MA0066.10.957
MA0067.10.686
MA0068.10.946
MA0069.10.883
MA0070.10.393
MA0071.10.722
MA0072.10.9
MA0073.10.831
MA0074.10.073
MA0076.10.0141
MA0077.10.0612
MA0078.10.985
MA0079.20.908
MA0080.22.56833e-8
MA0081.10.00424
MA0083.11.36026e-5
MA0084.10.589
MA0087.10.779
MA0088.10.442
MA0090.18.70695e-4
MA0091.10.137
MA0092.10.448
MA0093.10.421
MA0099.20.0256
MA0100.10.335
MA0101.10.0801
MA0102.20.429
MA0103.12.52851e-4
MA0104.20.997
MA0105.10.419
MA0106.10.158
MA0107.10.0975
MA0108.20.0131
MA0111.10.11
MA0112.20.0489
MA0113.10.43
MA0114.10.199
MA0115.10.182
MA0116.10.923
MA0117.10.395
MA0119.10.135
MA0122.10.599
MA0124.10.207
MA0125.10.0326
MA0131.10.819
MA0135.10.356
MA0136.16.8693e-12
MA0137.20.332
MA0138.20.377
MA0139.10.676
MA0140.10.677
MA0141.10.574
MA0142.10.275
MA0143.10.434
MA0144.10.19
MA0145.10.823
MA0146.10.357
MA0147.10.987
MA0148.10.969
MA0149.10.815
MA0150.10.0813
MA0152.10.00727
MA0153.10.382
MA0154.10.664
MA0155.10.534
MA0156.18.07154e-9
MA0157.10.314
MA0159.10.775
MA0160.10.452
MA0162.10.558
MA0163.10.392
MA0164.10.382
MA0258.10.771
MA0259.10.84



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: CNhs12369

Novel motifP-value
10.664
100.818
1000.519
1010.526
1020.0523
1030.825
1040.913
1050.216
1060.957
1070.618
1080.0739
1090.464
110.868
1100.114
1110.273
1120.44
1130.00123
1140.957
1150.384
1160.0706
1170.652
1180.413
1190.199
120.882
1200.228
1210.822
1220.0283
1234.06629e-4
1240.172
1250.169
1260.356
1270.47
1280.329
1290.596
130.941
1300.528
1310.592
1320.646
1330.891
1340.211
1350.412
1360.869
1370.175
1380.586
1390.553
140.185
1400.837
1410.935
1420.928
1430.857
1440.289
1450.984
1460.726
1470.0735
1480.862
1490.0957
150.739
1500.593
1510.958
1520.349
1530.272
1540.902
1550.0114
1560.162
1570.887
1580.00563
1590.176
160.0185
1600.933
1610.571
1620.776
1630.257
1640.0708
1650.664
1660.0319
1670.322
1680.664
1690.105
170.786
180.112
190.02
20.238
200.687
210.103
220.212
230.13
240.18
250.0661
260.758
270.863
280.129
290.283
30.779
300.49
310.607
321.18215e-13
330.715
340.764
350.928
360.0135
370.176
380.195
390.18
40.0141
400.0317
410.638
420.164
430.984
440.732
450.885
460.803
470.19
480.487
490.147
50.982
500.811
510.875
520.673
530.0704
540.745
550.106
560.66
570.596
580.133
590.638
60.686
600.698
610.667
620.217
630.759
640.485
650.973
660.123
670.5
680.264
690.672
70.0923
700.928
710.651
720.372
730.164
740.0591
750.701
760.396
770.157
780.0188
790.0237
80.426
800.325
810.604
820.892
830.721
840.978
850.0648
860.256
870.414
880.533
890.117
90.564
900.603
910.865
920.211
930.608
940.886
950.616
960.484
970.302
980.106
990.292



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: CNhs12369


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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