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FF:11533-120A3: 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:Amniotic Epithelial Cells, 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 stageNA
sexNA
ageNA
cell typeamniotic epithelial 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 numberSC7105
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-penis-0.117
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-lymphoma0.139
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs11341

Jaspar motifP-value
MA0002.20.244
MA0003.10.455
MA0004.10.494
MA0006.10.0458
MA0007.10.0118
MA0009.10.62
MA0014.10.453
MA0017.10.922
MA0018.20.0374
MA0019.10.0546
MA0024.10.454
MA0025.10.052
MA0027.10.795
MA0028.10.402
MA0029.10.0483
MA0030.10.0277
MA0031.10.0261
MA0035.20.267
MA0038.14.06491e-4
MA0039.20.0263
MA0040.10.952
MA0041.10.752
MA0042.10.314
MA0043.10.00297
MA0046.10.674
MA0047.20.308
MA0048.10.501
MA0050.11.00585e-7
MA0051.13.99492e-7
MA0052.10.509
MA0055.10.00508
MA0057.10.456
MA0058.10.113
MA0059.10.419
MA0060.11.32285e-5
MA0061.10.163
MA0062.20.0156
MA0065.20.286
MA0066.10.405
MA0067.10.00135
MA0068.10.21
MA0069.10.724
MA0070.10.0262
MA0071.10.935
MA0072.10.949
MA0073.10.311
MA0074.10.954
MA0076.10.0315
MA0077.10.727
MA0078.10.926
MA0079.20.4
MA0080.21.77969e-8
MA0081.10.00515
MA0083.10.19
MA0084.10.321
MA0087.10.423
MA0088.10.801
MA0090.18.80258e-6
MA0091.10.969
MA0092.10.434
MA0093.10.364
MA0099.27.04264e-5
MA0100.10.61
MA0101.10.0715
MA0102.21.34184e-4
MA0103.10.00166
MA0104.20.136
MA0105.10.581
MA0106.10.146
MA0107.10.0143
MA0108.20.343
MA0111.10.711
MA0112.20.206
MA0113.10.00863
MA0114.10.397
MA0115.10.752
MA0116.10.945
MA0117.10.36
MA0119.10.456
MA0122.10.441
MA0124.10.023
MA0125.10.00757
MA0131.10.712
MA0135.10.465
MA0136.11.0197e-7
MA0137.20.00755
MA0138.20.657
MA0139.10.641
MA0140.10.426
MA0141.10.787
MA0142.10.491
MA0143.10.195
MA0144.10.921
MA0145.10.159
MA0146.10.0559
MA0147.10.337
MA0148.10.582
MA0149.10.691
MA0150.10.323
MA0152.10.443
MA0153.10.435
MA0154.10.492
MA0155.10.425
MA0156.12.82615e-5
MA0157.10.0156
MA0159.10.736
MA0160.10.957
MA0162.10.0525
MA0163.10.358
MA0164.10.14
MA0258.10.936
MA0259.10.239



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: CNhs11341

Novel motifP-value
10.366
100.584
1000.806
1010.506
1020.996
1030.17
1040.881
1050.0895
1060.0472
1070.051
1080.379
1090.0497
110.633
1100.0958
1110.827
1120.723
1139.44878e-5
1140.875
1150.361
1160.883
1170.31
1180.257
1190.413
120.711
1200.346
1210.16
1220.227
1230.169
1240.182
1250.308
1260.149
1270.561
1280.672
1290.172
130.277
1300.604
1310.0225
1320.411
1330.486
1340.0914
1350.533
1360.118
1370.12
1380.275
1390.153
140.985
1400.631
1410.6
1420.558
1430.734
1440.944
1450.681
1460.0466
1470.18
1480.121
1490.129
150.974
1500.141
1510.326
1520.0636
1530.136
1540.444
1550.2
1560.245
1570.62
1580.413
1590.451
160.193
1600.0701
1610.213
1620.197
1630.475
1640.949
1650.808
1660.15
1670.221
1680.533
1690.0599
170.144
180.36
190.522
20.0802
200.892
210.361
220.142
230.134
240.844
250.736
260.412
270.463
280.853
290.766
30.989
300.107
310.819
320.13
330.113
340.515
350.0391
360.183
370.963
380.725
390.156
40.513
400.0461
410.776
420.901
430.309
440.921
450.102
460.777
470.736
480.183
490.289
50.996
500.363
510.399
520.259
530.652
540.563
550.224
560.339
570.502
580.653
590.174
60.759
600.541
610.437
620.802
630.492
640.225
650.438
660.115
670.597
680.897
690.00108
70.3
700.792
710.468
720.705
730.0762
740.13
750.503
760.153
770.0319
780.417
790.553
80.72
800.61
810.672
820.547
830.985
840.519
850.586
860.28
870.941
880.227
890.185
90.391
900.354
910.266
920.537
930.57
940.668
950.554
960.577
970.269
980.965
990.0202



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: CNhs11341


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)
0000066 (epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002371 (somatic cell)
0002536 (amniotic epithelial 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)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000926 (mesoderm)
0001062 (anatomical entity)
0002050 (embryonic structure)
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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