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FF:12823-136I6: 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 17:27, 29 March 2012


Name:H9 Embryoid body cells, melanocytic induction, day00, biol_rep3 (H9EB-3 d0)
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-penis0.074
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-lymphoma0.547
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: CNhs12908

Jaspar motifP-value
MA0002.22.23214e-4
MA0003.10.19
MA0004.10.736
MA0006.10.519
MA0007.10.888
MA0009.10.894
MA0014.10.777
MA0017.10.811
MA0018.20.848
MA0019.10.411
MA0024.14.65633e-6
MA0025.10.749
MA0027.10.538
MA0028.10.32
MA0029.10.7
MA0030.10.322
MA0031.10.203
MA0035.20.196
MA0038.10.00182
MA0039.20.0316
MA0040.10.784
MA0041.10.952
MA0042.10.988
MA0043.10.349
MA0046.10.039
MA0047.20.188
MA0048.10.867
MA0050.13.07764e-10
MA0051.13.67129e-5
MA0052.10.177
MA0055.10.392
MA0057.10.408
MA0058.10.724
MA0059.10.964
MA0060.11.23242e-13
MA0061.10.00534
MA0062.20.439
MA0065.20.618
MA0066.10.772
MA0067.10.0744
MA0068.10.017
MA0069.10.594
MA0070.10.255
MA0071.10.883
MA0072.10.973
MA0073.10.909
MA0074.10.869
MA0076.10.406
MA0077.10.0508
MA0078.10.621
MA0079.20.154
MA0080.21.2001e-12
MA0081.10.0174
MA0083.10.394
MA0084.10.593
MA0087.10.737
MA0088.10.511
MA0090.10.477
MA0091.10.0206
MA0092.10.0875
MA0093.10.605
MA0099.21.00075e-11
MA0100.10.77
MA0101.10.045
MA0102.25.68709e-4
MA0103.10.0494
MA0104.20.844
MA0105.10.0053
MA0106.10.989
MA0107.10.0165
MA0108.21.27522e-11
MA0111.10.774
MA0112.22.44941e-4
MA0113.10.0655
MA0114.10.682
MA0115.10.32
MA0116.10.0175
MA0117.10.493
MA0119.19.37079e-4
MA0122.10.809
MA0124.10.852
MA0125.10.0176
MA0131.10.676
MA0135.10.121
MA0136.15.11883e-11
MA0137.20.188
MA0138.20.977
MA0139.10.811
MA0140.10.89
MA0141.10.587
MA0142.16.55845e-15
MA0143.14.00713e-6
MA0144.10.0257
MA0145.10.244
MA0146.10.48
MA0147.10.755
MA0148.10.0459
MA0149.10.106
MA0150.12.13761e-4
MA0152.10.638
MA0153.10.166
MA0154.10.0383
MA0155.10.398
MA0156.12.92482e-6
MA0157.10.0841
MA0159.10.16
MA0160.10.209
MA0162.10.957
MA0163.12.20014e-4
MA0164.10.643
MA0258.10.0965
MA0259.10.542



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: CNhs12908

Novel motifP-value
10.122
100.0207
1000.952
1010.461
1020.75
1030.173
1040.602
1050.132
1060.0838
1070.5
1080.904
1090.233
110.202
1100.337
1110.0113
1120.45
1130.238
1140.0117
1150.295
1160.836
1170.15
1180.604
1190.196
120.912
1200.373
1210.78
1220.993
1230.0967
1240.157
1250.609
1260.581
1270.576
1280.749
1290.383
130.722
1300.316
1310.906
1320.902
1330.0956
1340.478
1350.0266
1360.122
1370.303
1380.0851
1390.00285
140.556
1400.329
1410.3
1420.606
1430.00261
1440.756
1450.522
1460.471
1470.843
1480.049
1490.0242
150.0472
1500.551
1510.0828
1520.943
1530.407
1540.222
1550.874
1560.447
1570.806
1580.246
1590.514
160.425
1600.581
1610.919
1620.383
1630.446
1640.186
1650.297
1660.754
1670.0264
1680.24
1690.00223
170.349
180.285
190.257
20.611
200.643
210.479
220.18
230.0184
240.714
250.473
260.368
270.692
280.656
290.667
30.0722
300.664
310.865
320.0842
330.714
340.833
350.214
360.0613
370.356
380.286
390.606
40.79
400.833
410.11
420.259
430.0999
440.66
450.862
460.0706
470.753
480.693
490.0624
50.0948
500.928
510.776
520.669
530.239
540.546
550.0153
560.69
570.468
580.0616
590.458
60.862
600.182
610.866
620.0253
630.111
640.45
650.109
660.593
670.27
680.323
690.446
70.603
700.0233
710.0356
720.374
730.152
740.107
750.171
760.288
770.303
780.739
790.325
80.208
800.197
810.278
820.0763
830.287
840.942
850.0768
860.292
870.259
880.863
890.189
90.183
900.117
910.183
920.0268
930.424
940.0308
950.979
960.0133
970.583
980.287
990.326



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: CNhs12908


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)
0000055 (non-terminally differentiated cell)
0000066 (epithelial cell)
0000075 (columnar/cuboidal epithelial cell)
0000133 (neurectodermal cell)
0000147 (pigment cell)
0000148 (melanocyte)
0000219 (motile cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000325 (stuff accumulating cell)
0000333 (migratory neural crest cell)
0000541 (melanoblast)
0000548 (animal cell)
0000710 (neurecto-epithelial cell)
0002077 (ecto-epithelial cell)
0002321 (embryonic cell)
0002322 (embryonic stem cell)
0002371 (somatic 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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