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FF:12724-135G6: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100669
|fonse_cell_line=FF:0100669
|fonse_cell_line_closure=FF:0100669
|fonse_cell_line_closure=FF:0100669

Revision as of 17:25, 29 March 2012


Name:H9 Embryonic Stem cells, biol_rep2 (H9ES-2)
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueunclassifiable
dev stageNA
sexfemale
ageNA
cell typestem cell
cell lineH9
companyNA
collaborationSusan Zabierowski (Wistar Institute)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
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-penis0.0499
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-lymphoma0.576
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: CNhs12824

Jaspar motifP-value
MA0002.21.41551e-4
MA0003.10.134
MA0004.10.472
MA0006.10.627
MA0007.10.919
MA0009.10.616
MA0014.10.467
MA0017.10.208
MA0018.20.269
MA0019.10.452
MA0024.13.96943e-5
MA0025.10.341
MA0027.10.477
MA0028.10.211
MA0029.10.427
MA0030.10.984
MA0031.10.545
MA0035.20.581
MA0038.18.67494e-4
MA0039.20.0404
MA0040.10.842
MA0041.10.93
MA0042.10.79
MA0043.10.774
MA0046.10.934
MA0047.20.28
MA0048.10.47
MA0050.11.17577e-8
MA0051.14.557e-5
MA0052.10.323
MA0055.10.0937
MA0057.10.456
MA0058.10.414
MA0059.10.869
MA0060.11.49199e-16
MA0061.10.0194
MA0062.20.974
MA0065.20.824
MA0066.10.481
MA0067.10.348
MA0068.10.116
MA0069.10.412
MA0070.10.0379
MA0071.10.706
MA0072.10.703
MA0073.10.926
MA0074.10.696
MA0076.10.189
MA0077.10.113
MA0078.10.689
MA0079.20.0889
MA0080.22.38998e-11
MA0081.10.0571
MA0083.10.343
MA0084.10.422
MA0087.10.936
MA0088.10.636
MA0090.10.366
MA0091.10.0229
MA0092.10.0661
MA0093.10.356
MA0099.26.52097e-11
MA0100.10.576
MA0101.10.136
MA0102.20.00185
MA0103.10.0726
MA0104.20.737
MA0105.17.42083e-4
MA0106.10.954
MA0107.10.06
MA0108.22.54616e-6
MA0111.10.63
MA0112.25.95775e-5
MA0113.10.0775
MA0114.10.554
MA0115.10.687
MA0116.10.00488
MA0117.10.897
MA0119.10.00117
MA0122.10.702
MA0124.10.926
MA0125.10.0284
MA0131.10.833
MA0135.10.236
MA0136.16.90979e-9
MA0137.20.389
MA0138.20.609
MA0139.10.89
MA0140.10.403
MA0141.10.554
MA0142.15.40353e-14
MA0143.15.59461e-5
MA0144.10.0362
MA0145.10.188
MA0146.10.42
MA0147.10.826
MA0148.10.0639
MA0149.10.141
MA0150.19.26455e-4
MA0152.10.398
MA0153.10.937
MA0154.10.0268
MA0155.10.704
MA0156.15.52004e-4
MA0157.10.265
MA0159.10.0992
MA0160.10.307
MA0162.10.542
MA0163.12.19049e-6
MA0164.10.815
MA0258.10.0627
MA0259.10.741



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: CNhs12824

Novel motifP-value
10.0961
100.0161
1000.897
1010.32
1020.54
1030.17
1040.638
1050.25
1060.0354
1070.272
1080.89
1090.351
110.149
1100.338
1110.0139
1120.26
1130.0427
1140.0191
1150.273
1160.954
1170.298
1180.544
1190.149
120.999
1200.607
1210.808
1220.927
1230.119
1240.12
1250.732
1260.873
1270.677
1280.558
1290.429
130.609
1300.153
1310.469
1320.753
1330.0805
1340.376
1350.0304
1360.175
1370.355
1380.199
1390.00465
140.613
1400.113
1410.547
1420.587
1430.0156
1440.469
1450.413
1460.354
1470.729
1480.00441
1490.0104
150.0695
1500.714
1510.0555
1520.674
1530.189
1540.158
1550.853
1560.777
1570.672
1580.652
1590.779
160.374
1600.256
1610.992
1620.513
1630.662
1640.214
1650.281
1660.634
1670.0151
1680.288
1695.4759e-4
170.315
180.325
190.153
20.539
200.974
210.503
220.213
230.019
240.84
250.323
260.211
270.472
280.812
290.869
30.0772
300.841
310.834
320.0394
330.683
340.858
350.303
360.0466
370.296
380.324
390.483
40.896
400.581
410.19
420.23
430.122
440.752
450.723
460.0604
470.737
480.558
490.0836
50.07
500.875
510.772
520.42
530.153
540.443
550.023
560.618
570.397
580.0645
590.265
60.67
600.0937
610.866
620.0253
630.117
640.294
650.102
660.284
670.165
680.669
690.705
70.302
700.0101
710.0302
720.476
730.18
740.186
750.344
760.44
770.278
780.488
790.304
80.124
800.114
810.257
820.0403
830.818
840.96
850.0357
860.663
870.246
880.572
890.142
90.21
900.155
910.137
920.0267
930.288
940.047
950.713
960.027
970.664
980.316
990.693



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: CNhs12824


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)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002321 (embryonic cell)
0002322 (embryonic stem cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000922 (embryo)
0001062 (anatomical entity)

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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