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FF:11627-122B7: 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 17:11, 29 March 2012


Name:Mesenchymal Stem Cells - amniotic membrane, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueamnion
dev stageNA
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-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-lymphoma-0.0947
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs12104

Jaspar motifP-value
MA0002.20.911
MA0003.10.253
MA0004.10.71
MA0006.10.11
MA0007.10.357
MA0009.10.686
MA0014.10.477
MA0017.10.566
MA0018.21.43312e-7
MA0019.10.382
MA0024.12.05184e-4
MA0025.10.00936
MA0027.10.795
MA0028.10.00758
MA0029.10.522
MA0030.10.0425
MA0031.10.087
MA0035.20.692
MA0038.10.0773
MA0039.20.167
MA0040.10.668
MA0041.10.462
MA0042.10.499
MA0043.11.29419e-6
MA0046.10.378
MA0047.20.122
MA0048.10.876
MA0050.10.504
MA0051.10.258
MA0052.10.569
MA0055.10.713
MA0057.10.139
MA0058.10.807
MA0059.10.948
MA0060.16.94485e-6
MA0061.10.813
MA0062.21.31729e-7
MA0065.20.552
MA0066.10.147
MA0067.10.00684
MA0068.10.308
MA0069.10.231
MA0070.10.678
MA0071.10.159
MA0072.10.646
MA0073.10.985
MA0074.10.476
MA0076.19.8922e-5
MA0077.10.917
MA0078.10.791
MA0079.20.487
MA0080.22.40537e-6
MA0081.10.0111
MA0083.16.80638e-8
MA0084.10.881
MA0087.10.676
MA0088.10.684
MA0090.10.00199
MA0091.10.00656
MA0092.10.0908
MA0093.10.701
MA0099.20.816
MA0100.10.224
MA0101.10.0497
MA0102.20.0448
MA0103.10.237
MA0104.20.124
MA0105.10.453
MA0106.10.0742
MA0107.10.144
MA0108.20.068
MA0111.10.702
MA0112.20.00194
MA0113.10.913
MA0114.10.535
MA0115.10.36
MA0116.10.784
MA0117.10.495
MA0119.10.148
MA0122.10.196
MA0124.10.0614
MA0125.10.9
MA0131.10.0394
MA0135.10.677
MA0136.11.46335e-9
MA0137.20.00232
MA0138.20.507
MA0139.10.343
MA0140.10.9
MA0141.10.593
MA0142.10.224
MA0143.10.815
MA0144.10.451
MA0145.10.279
MA0146.10.0855
MA0147.10.0969
MA0148.10.438
MA0149.10.931
MA0150.10.565
MA0152.10.955
MA0153.10.44
MA0154.10.365
MA0155.10.0726
MA0156.11.56128e-7
MA0157.10.194
MA0159.10.194
MA0160.10.911
MA0162.10.0495
MA0163.10.063
MA0164.10.867
MA0258.10.0881
MA0259.10.193



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: CNhs12104

Novel motifP-value
10.941
100.8
1000.76
1010.797
1020.164
1030.507
1040.367
1050.633
1060.0291
1070.0592
1080.235
1090.328
110.28
1100.296
1110.697
1120.168
1130.972
1140.0886
1150.198
1160.063
1170.782
1180.958
1190.476
120.514
1200.183
1210.459
1220.105
1230.0599
1240.836
1250.767
1260.994
1270.516
1280.292
1290.997
130.502
1300.344
1310.287
1320.726
1330.959
1340.799
1350.491
1360.879
1370.311
1380.3
1390.64
140.707
1400.684
1410.332
1420.985
1430.302
1440.766
1450.364
1460.675
1470.0555
1480.849
1490.00253
150.868
1500.554
1510.396
1520.0572
1530.572
1540.833
1550.0517
1560.474
1570.77
1580.189
1590.731
160.0711
1600.0743
1610.463
1620.497
1630.934
1640.418
1650.0641
1660.25
1670.819
1680.324
1690.0171
170.232
180.181
190.00874
20.125
200.184
210.248
220.0598
230.0588
240.531
250.416
260.405
270.0631
280.475
290.886
30.461
300.286
310.59
324.62891e-7
330.711
340.414
350.79
360.122
370.0748
380.809
390.617
40.799
400.53
410.885
420.602
430.219
440.0403
450.309
460.12
470.62
480.591
490.362
50.676
500.495
510.59
520.694
530.634
540.387
550.982
560.5
570.548
580.762
590.0736
60.157
600.662
610.934
620.579
630.266
640.513
650.038
660.956
670.879
680.903
690.811
70.757
700.034
710.265
720.755
730.0423
740.0869
750.994
760.238
770.0808
780.916
790.00258
80.114
800.254
810.524
820.161
830.0424
840.453
850.0139
860.852
870.427
880.612
890.0192
90.277
900.44
910.318
920.0737
930.599
940.241
950.502
960.736
970.582
980.856
990.0121



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: CNhs12104


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)
0002537 (amnion mesenchymal stem cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000158 (membranous layer)
0000305 (amnion)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000478 (extraembryonic structure)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000926 (mesoderm)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002384 (connective tissue)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004871 (somatic layer of lateral plate mesoderm)
0004923 (organ component layer)
0005423 (developing anatomical structure)
0005631 (extraembryonic membrane)

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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