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FF:11539-120A9: 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 16:46, 29 March 2012


Name:Mesenchymal Stem Cells - umbilical, 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 stageNA
sexNA
ageNA
cell typemesenchymal stem cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberSC7535
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-penis0.0108
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-0.488
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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: CNhs11347

Jaspar motifP-value
MA0002.20.779
MA0003.10.148
MA0004.10.986
MA0006.10.222
MA0007.10.0191
MA0009.10.357
MA0014.10.763
MA0017.10.0974
MA0018.20.0234
MA0019.10.287
MA0024.12.86915e-5
MA0025.10.0504
MA0027.10.341
MA0028.10.363
MA0029.10.308
MA0030.10.329
MA0031.10.105
MA0035.20.382
MA0038.10.799
MA0039.20.733
MA0040.10.49
MA0041.10.335
MA0042.10.683
MA0043.10.0287
MA0046.10.122
MA0047.20.485
MA0048.10.666
MA0050.10.00213
MA0051.11.6027e-4
MA0052.10.024
MA0055.10.416
MA0057.10.422
MA0058.10.957
MA0059.10.771
MA0060.10.00101
MA0061.10.81
MA0062.20.00553
MA0065.20.0219
MA0066.10.192
MA0067.10.0712
MA0068.10.556
MA0069.10.0828
MA0070.10.168
MA0071.10.00525
MA0072.10.0824
MA0073.10.57
MA0074.10.0473
MA0076.10.135
MA0077.10.683
MA0078.10.708
MA0079.20.736
MA0080.28.48607e-7
MA0081.10.0198
MA0083.10.805
MA0084.10.111
MA0087.10.344
MA0088.10.627
MA0090.10.377
MA0091.10.00236
MA0092.10.218
MA0093.10.982
MA0099.20.0596
MA0100.10.0887
MA0101.10.17
MA0102.20.544
MA0103.10.409
MA0104.20.453
MA0105.10.296
MA0106.10.58
MA0107.10.2
MA0108.20.18
MA0111.10.901
MA0112.29.07734e-4
MA0113.11.74365e-4
MA0114.10.0709
MA0115.10.984
MA0116.10.0679
MA0117.10.502
MA0119.10.165
MA0122.10.697
MA0124.10.71
MA0125.10.226
MA0131.10.353
MA0135.10.639
MA0136.11.43014e-6
MA0137.20.722
MA0138.20.272
MA0139.10.709
MA0140.10.48
MA0141.10.112
MA0142.10.349
MA0143.10.623
MA0144.10.45
MA0145.10.139
MA0146.10.00524
MA0147.10.483
MA0148.10.95
MA0149.10.411
MA0150.10.318
MA0152.10.505
MA0153.10.157
MA0154.10.0691
MA0155.10.0966
MA0156.11.27507e-6
MA0157.10.245
MA0159.10.0728
MA0160.10.349
MA0162.10.139
MA0163.10.00203
MA0164.10.727
MA0258.10.0158
MA0259.10.44



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: CNhs11347

Novel motifP-value
10.622
100.979
1000.837
1010.977
1020.72
1030.232
1040.781
1050.414
1060.0678
1070.0528
1080.272
1090.218
110.131
1100.244
1110.616
1120.932
1130.0972
1140.6
1150.329
1160.0908
1170.402
1180.324
1190.865
120.798
1200.111
1210.921
1220.407
1230.00248
1240.483
1250.111
1260.412
1270.502
1280.202
1290.51
130.621
1300.47
1310.37
1320.183
1330.573
1340.643
1350.582
1360.531
1370.0734
1380.35
1390.00492
140.78
1400.168
1410.52
1420.488
1430.153
1440.117
1450.512
1460.352
1470.29
1480.831
1490.00108
150.882
1500.459
1510.401
1520.0682
1530.387
1540.429
1550.468
1560.689
1570.0887
1580.974
1590.968
160.0283
1600.0575
1610.348
1620.294
1630.955
1640.537
1650.555
1660.397
1670.341
1680.427
1690.0371
170.234
180.0759
190.0297
20.263
200.902
210.123
220.0423
230.157
240.403
250.587
260.219
270.487
280.287
290.591
30.278
300.224
310.237
321.26866e-15
330.894
340.151
350.875
360.563
370.0997
380.639
390.264
40.945
400.221
410.143
420.95
430.124
440.374
450.308
460.148
470.533
480.222
490.159
50.778
500.334
510.186
520.614
530.633
540.361
550.632
560.309
570.884
580.856
590.0418
60.401
600.43
610.539
620.422
630.302
640.295
650.0687
660.567
670.865
680.0325
690.189
70.865
700.0453
710.128
720.883
730.0524
740.839
750.271
760.796
770.0267
780.66
790.00453
80.186
800.69
810.847
820.131
830.948
840.199
850.0772
860.845
870.584
880.247
890.0323
90.12
900.422
910.802
920.142
930.613
940.306
950.345
960.68
970.649
980.411
990.109



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: CNhs11347


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)
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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