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FF:11547-120B8: 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 - amniotic membrane, donor1
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 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-0.0418
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-0.216
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs11349

Jaspar motifP-value
MA0002.20.0821
MA0003.10.26
MA0004.10.589
MA0006.10.0844
MA0007.10.473
MA0009.10.423
MA0014.10.0932
MA0017.10.202
MA0018.24.28326e-7
MA0019.10.449
MA0024.13.65098e-6
MA0025.10.00313
MA0027.10.841
MA0028.10.13
MA0029.10.665
MA0030.10.196
MA0031.10.0482
MA0035.20.143
MA0038.10.15
MA0039.20.00981
MA0040.10.937
MA0041.10.66
MA0042.10.727
MA0043.12.44866e-5
MA0046.10.623
MA0047.20.0575
MA0048.10.898
MA0050.10.872
MA0051.10.734
MA0052.10.336
MA0055.10.471
MA0057.10.308
MA0058.10.582
MA0059.10.238
MA0060.13.15846e-8
MA0061.10.0186
MA0062.21.6444e-5
MA0065.20.0969
MA0066.10.868
MA0067.10.0679
MA0068.10.0693
MA0069.10.217
MA0070.10.887
MA0071.10.933
MA0072.10.883
MA0073.10.65
MA0074.10.782
MA0076.10.0584
MA0077.10.57
MA0078.10.89
MA0079.20.767
MA0080.22.0048e-8
MA0081.10.0313
MA0083.17.9816e-9
MA0084.10.782
MA0087.10.952
MA0088.10.171
MA0090.18.00162e-6
MA0091.10.112
MA0092.10.314
MA0093.10.733
MA0099.20.0797
MA0100.10.18
MA0101.10.00283
MA0102.20.174
MA0103.10.0058
MA0104.20.00236
MA0105.10.323
MA0106.10.171
MA0107.10.00472
MA0108.20.262
MA0111.10.256
MA0112.20.163
MA0113.10.624
MA0114.10.14
MA0115.10.0263
MA0116.10.0784
MA0117.10.467
MA0119.10.591
MA0122.10.403
MA0124.10.933
MA0125.10.966
MA0131.10.279
MA0135.10.452
MA0136.12.1118e-9
MA0137.20.0394
MA0138.20.98
MA0139.10.414
MA0140.10.153
MA0141.10.11
MA0142.10.0404
MA0143.10.662
MA0144.10.172
MA0145.10.32
MA0146.10.734
MA0147.10.00172
MA0148.10.281
MA0149.10.162
MA0150.10.0857
MA0152.10.071
MA0153.10.508
MA0154.10.514
MA0155.10.15
MA0156.19.74308e-8
MA0157.10.142
MA0159.10.782
MA0160.10.0721
MA0162.10.141
MA0163.10.989
MA0164.10.952
MA0258.10.437
MA0259.10.0193



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: CNhs11349

Novel motifP-value
10.115
100.616
1000.257
1010.615
1020.0823
1030.704
1040.752
1050.181
1060.458
1070.399
1080.958
1090.919
110.461
1100.92
1110.472
1120.542
1130.656
1140.576
1150.0309
1160.0888
1170.32
1180.441
1190.439
120.326
1200.288
1210.739
1220.254
1230.0045
1240.321
1250.319
1260.441
1270.969
1280.972
1290.0893
130.0896
1300.266
1310.275
1320.79
1330.436
1340.383
1350.382
1360.569
1370.166
1380.791
1390.765
140.291
1400.208
1410.0541
1420.805
1430.655
1440.826
1450.217
1460.555
1470.111
1480.343
1490.0182
150.219
1500.42
1510.74
1520.018
1530.522
1540.395
1550.00686
1560.598
1570.637
1580.0517
1590.746
160.163
1600.755
1610.2
1620.311
1630.94
1640.73
1650.413
1660.0486
1670.812
1680.919
1690.142
170.94
180.287
190.0182
20.127
200.238
210.107
220.339
230.527
240.774
250.0763
260.292
270.342
280.382
290.813
30.524
300.151
310.692
322.95237e-7
330.28
340.41
350.733
360.0504
370.358
380.238
390.223
40.441
400.333
410.232
420.166
430.574
440.4
450.335
460.878
470.373
480.418
490.418
50.457
500.667
510.955
520.973
530.179
540.541
550.192
560.833
570.537
580.173
590.382
60.23
600.39
610.927
620.247
630.901
640.306
650.837
660.47
670.265
680.891
690.523
70.0661
700.756
710.977
720.872
730.0539
740.412
750.694
760.254
770.16
780.263
790.00404
80.72
800.271
810.863
820.358
830.0861
840.706
850.384
860.606
870.488
880.943
890.28
90.479
900.488
910.888
920.589
930.547
940.909
950.801
960.716
970.538
980.255
990.0413



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: CNhs11349


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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