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FF:11548-120B9: 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 16:38, 29 March 2012


Name:Mesenchymal Stem Cells - Wharton's Jelly, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueumbilical cord
dev stagefetus
sexfemale
age?
cell typemesenchymal stem cell
cell lineNA
companyCET
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-0.0292
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-0.415
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs11057

Jaspar motifP-value
MA0002.20.382
MA0003.10.933
MA0004.10.281
MA0006.10.264
MA0007.10.608
MA0009.10.00545
MA0014.10.5
MA0017.10.176
MA0018.21.34977e-5
MA0019.10.599
MA0024.12.90397e-11
MA0025.10.0122
MA0027.10.574
MA0028.10.793
MA0029.10.634
MA0030.10.815
MA0031.10.461
MA0035.20.323
MA0038.10.022
MA0039.21.72589e-4
MA0040.10.355
MA0041.10.578
MA0042.10.96
MA0043.10.0191
MA0046.10.327
MA0047.20.474
MA0048.10.0576
MA0050.13.47203e-6
MA0051.10.00792
MA0052.10.00213
MA0055.10.874
MA0057.10.569
MA0058.10.288
MA0059.10.819
MA0060.13.17291e-15
MA0061.10.124
MA0062.20.00141
MA0065.20.0225
MA0066.10.424
MA0067.10.0735
MA0068.10.0631
MA0069.10.0771
MA0070.10.554
MA0071.10.99
MA0072.10.817
MA0073.10.812
MA0074.10.649
MA0076.10.5
MA0077.10.867
MA0078.10.664
MA0079.20.996
MA0080.21.34344e-9
MA0081.10.0131
MA0083.10.0301
MA0084.10.552
MA0087.10.904
MA0088.10.26
MA0090.12.60338e-6
MA0091.10.42
MA0092.10.177
MA0093.10.502
MA0099.20.00317
MA0100.10.128
MA0101.10.334
MA0102.20.714
MA0103.10.002
MA0104.20.0472
MA0105.10.0488
MA0106.10.126
MA0107.10.673
MA0108.20.906
MA0111.10.186
MA0112.20.877
MA0113.10.89
MA0114.10.182
MA0115.10.0326
MA0116.10.00364
MA0117.10.51
MA0119.10.499
MA0122.10.337
MA0124.10.553
MA0125.10.0519
MA0131.10.497
MA0135.10.0625
MA0136.12.63559e-10
MA0137.20.261
MA0138.20.138
MA0139.10.804
MA0140.10.933
MA0141.10.127
MA0142.10.0752
MA0143.10.973
MA0144.10.497
MA0145.10.575
MA0146.10.136
MA0147.10.0751
MA0148.10.882
MA0149.10.905
MA0150.10.424
MA0152.10.199
MA0153.10.905
MA0154.10.081
MA0155.10.274
MA0156.11.49684e-4
MA0157.10.442
MA0159.10.29
MA0160.10.0378
MA0162.10.463
MA0163.10.465
MA0164.10.277
MA0258.10.877
MA0259.10.161



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: CNhs11057

Novel motifP-value
10.414
100.552
1000.927
1010.645
1020.183
1030.463
1040.915
1050.139
1060.129
1070.305
1080.48
1090.364
110.264
1100.679
1110.182
1120.89
1130.00128
1140.956
1150.22
1160.227
1170.277
1180.271
1190.943
120.174
1200.971
1210.684
1220.18
1230.0805
1240.51
1250.468
1260.29
1270.946
1280.565
1290.188
130.497
1300.769
1310.0515
1320.643
1330.355
1340.317
1350.619
1360.631
1370.253
1380.982
1390.0286
140.0842
1400.464
1410.0433
1420.736
1430.756
1440.4
1450.886
1460.685
1470.326
1480.295
1490.0412
150.948
1500.228
1510.984
1520.0238
1530.189
1540.674
1551.78201e-4
1560.34
1570.681
1580.0077
1590.288
160.164
1600.233
1610.704
1620.388
1630.511
1640.129
1650.872
1660.0515
1670.454
1680.18
1690.75
170.991
180.219
190.715
20.779
200.563
210.843
220.844
230.429
240.843
250.0745
260.256
270.593
280.383
290.718
30.807
300.677
310.986
323.16451e-8
330.643
340.804
350.677
360.377
370.289
380.0534
390.319
40.297
400.198
410.333
420.14
430.404
440.802
450.666
460.516
470.129
480.479
490.0813
50.613
500.936
510.596
520.931
530.333
540.869
550.048
560.566
570.941
580.0209
590.279
60.453
600.322
610.299
620.0795
630.88
640.442
650.243
660.247
670.333
680.351
690.956
70.0582
700.676
710.887
720.542
730.0877
740.336
750.53
760.903
770.88
780.0898
790.0185
80.997
800.614
810.675
820.452
830.898
840.457
850.714
860.953
870.325
880.821
890.349
90.854
900.92
910.89
920.44
930.434
940.816
950.644
960.609
970.138
980.00417
990.046



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: CNhs11057


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)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002568 (mesenchymal stem cell of Wharton's jelly)
0002569 (mesenchymal stem cell of umbilical cord)

UBERON: Anatomy
0000061 (anatomical structure)
0000087 (inner cell mass)
0000091 (bilaminar disc)
0000358 (blastocyst)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000478 (extraembryonic structure)
0000479 (tissue)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002331 (umbilical cord)
0002384 (connective tissue)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003104 (mesenchyme)
0003422 (mesenchyme of umbilical cord)
0004120 (mesoderm-derived structure)
0005423 (developing anatomical structure)
0005728 (extraembryonic mesoderm)
0007806 (connecting stalk)
0008780 (inner cell mass derived epiblast)
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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