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FF:12236-129G4: 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 17:20, 29 March 2012


Name:amniotic membrane cells, 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
sexNA
ageNA
cell typeunclassifiable
cell lineNA
companyNA
collaborationHiroo Toyoda (Tokyo University of Pharm and life sciences)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
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-0.109
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-lymphoma0.278
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: CNhs12503

Jaspar motifP-value
MA0002.20.0562
MA0003.10.987
MA0004.10.965
MA0006.10.0681
MA0007.10.591
MA0009.10.371
MA0014.10.0419
MA0017.10.0996
MA0018.20.415
MA0019.10.0518
MA0024.19.70052e-7
MA0025.10.975
MA0027.10.863
MA0028.10.307
MA0029.10.671
MA0030.10.756
MA0031.10.839
MA0035.20.468
MA0038.10.0267
MA0039.20.00376
MA0040.10.833
MA0041.10.408
MA0042.10.829
MA0043.10.353
MA0046.10.561
MA0047.20.538
MA0048.10.177
MA0050.18.13848e-4
MA0051.10.0192
MA0052.10.41
MA0055.10.161
MA0057.10.532
MA0058.10.999
MA0059.10.0726
MA0060.13.42858e-5
MA0061.10.015
MA0062.20.764
MA0065.20.195
MA0066.10.684
MA0067.10.09
MA0068.10.0267
MA0069.10.867
MA0070.10.694
MA0071.10.258
MA0072.10.754
MA0073.10.527
MA0074.10.533
MA0076.10.636
MA0077.10.41
MA0078.10.233
MA0079.20.0803
MA0080.21.99845e-4
MA0081.10.095
MA0083.10.0352
MA0084.10.18
MA0087.10.451
MA0088.10.431
MA0090.12.99206e-6
MA0091.10.351
MA0092.10.226
MA0093.10.902
MA0099.20.0686
MA0100.10.643
MA0101.10.149
MA0102.20.668
MA0103.10.00568
MA0104.20.00323
MA0105.10.00304
MA0106.10.23
MA0107.10.0753
MA0108.20.00181
MA0111.10.903
MA0112.20.454
MA0113.10.778
MA0114.10.262
MA0115.10.112
MA0116.10.0182
MA0117.10.298
MA0119.10.0751
MA0122.10.546
MA0124.10.364
MA0125.10.0901
MA0131.10.694
MA0135.10.707
MA0136.10.0219
MA0137.20.0921
MA0138.20.513
MA0139.10.0856
MA0140.10.659
MA0141.10.00447
MA0142.10.492
MA0143.10.457
MA0144.10.665
MA0145.10.913
MA0146.10.0846
MA0147.10.00446
MA0148.10.497
MA0149.10.276
MA0150.10.114
MA0152.10.301
MA0153.10.705
MA0154.10.168
MA0155.10.632
MA0156.10.0808
MA0157.10.904
MA0159.10.269
MA0160.10.336
MA0162.10.473
MA0163.10.0338
MA0164.10.593
MA0258.10.0173
MA0259.10.356



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: CNhs12503

Novel motifP-value
10.0729
100.51
1000.678
1010.593
1020.978
1030.666
1040.588
1050.282
1060.049
1070.339
1080.379
1090.326
110.26
1100.505
1110.236
1120.423
1130.00476
1140.0618
1150.752
1160.122
1170.521
1180.317
1190.284
120.729
1200.345
1210.365
1220.493
1237.62243e-4
1240.0167
1250.793
1260.883
1270.887
1280.0345
1290.625
130.789
1300.949
1310.00781
1320.906
1330.977
1340.0274
1350.908
1360.00903
1370.291
1380.132
1390.00545
140.81
1400.903
1410.433
1420.103
1430.303
1440.864
1450.735
1460.0175
1470.157
1480.305
1490.98
150.802
1500.789
1510.968
1520.0649
1530.224
1540.223
1550.213
1560.429
1570.249
1580.509
1590.92
160.382
1600.945
1610.675
1620.453
1630.365
1640.943
1650.569
1660.827
1670.547
1680.43
1690.331
170.858
180.188
190.278
20.691
200.236
210.105
220.323
230.32
240.523
250.815
260.241
270.29
280.833
290.117
30.94
300.177
310.837
320.648
330.782
340.611
350.0126
360.0359
370.0384
380.424
390.372
40.852
400.974
410.292
420.789
430.234
440.529
450.176
460.0584
470.115
480.718
490.0623
50.89
500.725
510.771
520.752
530.094
540.941
550.329
560.971
570.617
580.278
590.777
60.808
600.068
610.986
620.224
630.147
640.887
650.257
660.761
670.367
680.21
690.368
70.811
700.136
710.252
720.643
730.264
740.0853
750.624
760.93
770.812
780.198
790.596
80.207
800.414
810.0162
820.052
830.802
840.49
850.118
860.0424
870.626
880.976
890.865
90.809
900.834
910.998
920.251
930.945
940.872
950.491
960.351
970.135
980.202
990.93



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: CNhs12503


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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