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FF:12237-129G5: 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 17:19, 29 March 2012


Name:amniotic membrane cells, donor3
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-penis0.193
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-0.398
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: CNhs12379

Jaspar motifP-value
MA0002.20.019
MA0003.10.788
MA0004.10.714
MA0006.10.315
MA0007.10.993
MA0009.10.779
MA0014.10.0307
MA0017.10.321
MA0018.20.0458
MA0019.10.043
MA0024.10.0187
MA0025.10.317
MA0027.10.152
MA0028.10.87
MA0029.10.332
MA0030.10.199
MA0031.10.874
MA0035.20.851
MA0038.10.348
MA0039.25.80705e-4
MA0040.10.775
MA0041.10.622
MA0042.10.634
MA0043.10.0361
MA0046.10.207
MA0047.20.548
MA0048.10.747
MA0050.12.48473e-6
MA0051.14.83316e-4
MA0052.10.491
MA0055.10.134
MA0057.10.892
MA0058.10.618
MA0059.10.621
MA0060.10.00799
MA0061.10.0132
MA0062.20.00537
MA0065.20.862
MA0066.10.489
MA0067.10.153
MA0068.10.738
MA0069.10.287
MA0070.10.313
MA0071.10.509
MA0072.10.34
MA0073.10.89
MA0074.10.857
MA0076.10.154
MA0077.10.0792
MA0078.10.969
MA0079.20.208
MA0080.29.41079e-11
MA0081.10.00581
MA0083.10.0098
MA0084.10.223
MA0087.10.855
MA0088.10.411
MA0090.11.00176e-7
MA0091.10.538
MA0092.10.26
MA0093.10.665
MA0099.24.93384e-8
MA0100.10.37
MA0101.13.25219e-4
MA0102.20.0622
MA0103.13.07614e-7
MA0104.20.258
MA0105.10.362
MA0106.10.439
MA0107.13.42055e-5
MA0108.20.896
MA0111.10.785
MA0112.20.54
MA0113.10.0247
MA0114.10.737
MA0115.10.774
MA0116.10.799
MA0117.10.586
MA0119.10.475
MA0122.10.204
MA0124.10.591
MA0125.10.214
MA0131.10.903
MA0135.10.342
MA0136.16.42326e-8
MA0137.20.0984
MA0138.20.585
MA0139.10.618
MA0140.10.628
MA0141.10.149
MA0142.10.979
MA0143.10.577
MA0144.10.559
MA0145.10.18
MA0146.10.00431
MA0147.10.497
MA0148.10.392
MA0149.10.89
MA0150.10.459
MA0152.10.242
MA0153.10.737
MA0154.10.681
MA0155.10.337
MA0156.16.85892e-8
MA0157.10.601
MA0159.10.498
MA0160.10.665
MA0162.10.354
MA0163.10.993
MA0164.10.145
MA0258.10.387
MA0259.10.536



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: CNhs12379

Novel motifP-value
10.482
100.43
1000.496
1010.52
1020.628
1030.0904
1040.548
1050.358
1060.999
1070.781
1080.129
1090.00101
110.779
1100.19
1110.422
1120.989
1135.26573e-4
1140.496
1150.909
1160.0955
1170.0149
1180.00199
1190.784
120.872
1200.183
1210.291
1220.788
1230.046
1240.0398
1250.973
1260.683
1270.934
1280.402
1290.317
130.41
1300.112
1310.0188
1320.26
1330.0123
1340.0413
1350.504
1360.0132
1370.217
1380.871
1390.405
140.933
1400.177
1410.653
1420.783
1430.254
1440.615
1450.569
1460.202
1470.984
1480.43
1490.382
150.789
1500.766
1510.108
1520.0976
1530.961
1540.589
1550.0167
1560.204
1570.564
1580.17
1590.858
160.0773
1600.155
1610.462
1620.806
1630.0819
1640.124
1650.345
1660.79
1670.894
1680.617
1690.02
170.423
180.809
190.678
20.207
200.215
210.244
220.0921
230.169
240.722
250.388
260.982
270.698
280.783
290.0817
30.262
300.252
310.928
320.906
330.526
340.0469
350.0468
360.0624
370.538
380.273
390.365
40.689
400.497
410.932
420.7
430.275
440.969
450.27
460.68
470.689
480.887
490.555
50.992
500.725
510.491
520.552
530.292
540.985
550.571
560.3
570.864
580.929
590.559
60.509
600.878
610.57
620.994
630.567
640.518
650.87
660.561
670.823
680.944
690.0667
70.588
700.0536
710.888
720.216
730.0813
740.131
750.042
760.406
770.212
780.523
790.8
80.572
800.497
810.771
820.979
830.978
840.31
850.0861
860.536
870.547
880.702
890.0865
90.945
900.583
910.302
920.966
930.528
940.879
950.464
960.425
970.143
980.387
990.641



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: CNhs12379


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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