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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000087,UBERON:0000091,UBERON:0000178,UBERON:0000179,UBERON:0000358,UBERON:0000463,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000478,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001009,UBERON:0001062,UBERON:0002050,UBERON:0002193,UBERON:0002331,UBERON:0002390,UBERON:0002532,UBERON:0003081,UBERON:0004120,UBERON:0004535,UBERON:0005423,UBERON:0005728,UBERON:0007806,UBERON:0008780
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000087,UBERON:0000091,UBERON:0000178,UBERON:0000179,UBERON:0000358,UBERON:0000463,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000478,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001009,UBERON:0001062,UBERON:0002050,UBERON:0002193,UBERON:0002331,UBERON:0002390,UBERON:0002532,UBERON:0003081,UBERON:0004120,UBERON:0004535,UBERON:0005423,UBERON:0005728,UBERON:0007806,UBERON:0008780
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000081,CL:0000144,CL:0000255,CL:0000548,CL:0000988,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000081,CL:0000144,CL:0000255,CL:0000548,CL:0000988,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101035
|fonse_cell_line=FF:0101035
|fonse_cell_line_closure=FF:0101035
|fonse_cell_line_closure=FF:0101035

Revision as of 16:37, 29 March 2012


Name:cord blood derived cell line:COBL-a 24h infection(-C)
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexNA
ageNA
cell typeunclassifiable
cell lineCOBL-a
companyNA
collaborationChieko Kai (University of Tokyo)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
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-penis0.162
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
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C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
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: CNhs11049

Jaspar motifP-value
MA0002.20.0343
MA0003.10.24
MA0004.10.688
MA0006.10.197
MA0007.10.253
MA0009.10.973
MA0014.10.574
MA0017.10.258
MA0018.22.25756e-11
MA0019.10.799
MA0024.17.78444e-4
MA0025.10.396
MA0027.10.484
MA0028.13.73469e-5
MA0029.10.0555
MA0030.10.269
MA0031.10.441
MA0035.20.00627
MA0038.10.00236
MA0039.20.444
MA0040.10.0429
MA0041.10.267
MA0042.10.243
MA0043.12.04815e-5
MA0046.10.087
MA0047.20.533
MA0048.10.125
MA0050.10.00928
MA0051.10.0115
MA0052.10.534
MA0055.10.0393
MA0057.10.185
MA0058.10.569
MA0059.10.638
MA0060.16.58777e-19
MA0061.13.57085e-12
MA0062.23.98272e-7
MA0065.20.471
MA0066.10.0221
MA0067.10.0395
MA0068.10.0164
MA0069.10.96
MA0070.10.568
MA0071.10.711
MA0072.10.016
MA0073.10.682
MA0074.10.514
MA0076.17.44874e-6
MA0077.10.735
MA0078.10.269
MA0079.20.369
MA0080.20.324
MA0081.10.934
MA0083.10.0281
MA0084.10.936
MA0087.10.278
MA0088.10.418
MA0090.19.96853e-4
MA0091.10.0403
MA0092.10.0971
MA0093.10.584
MA0099.20.462
MA0100.10.269
MA0101.11.97125e-14
MA0102.20.364
MA0103.10.0422
MA0104.20.0559
MA0105.11.11777e-4
MA0106.10.0746
MA0107.18.53403e-18
MA0108.20.787
MA0111.10.814
MA0112.20.00506
MA0113.10.0502
MA0114.10.824
MA0115.10.856
MA0116.10.607
MA0117.10.009
MA0119.10.193
MA0122.10.413
MA0124.10.537
MA0125.10.464
MA0131.10.042
MA0135.10.00373
MA0136.10.552
MA0137.20.0208
MA0138.20.0199
MA0139.10.752
MA0140.14.6195e-4
MA0141.10.423
MA0142.10.337
MA0143.10.0123
MA0144.10.905
MA0145.10.054
MA0146.10.206
MA0147.10.0648
MA0148.10.427
MA0149.10.617
MA0150.10.795
MA0152.10.309
MA0153.10.00214
MA0154.10.354
MA0155.10.0842
MA0156.10.0799
MA0157.10.159
MA0159.10.846
MA0160.10.227
MA0162.10.0378
MA0163.10.762
MA0164.10.43
MA0258.10.0538
MA0259.10.2



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: CNhs11049

Novel motifP-value
10.805
100.135
1000.249
1010.252
1020.965
1030.381
1040.822
1050.919
1060.0533
1070.027
1080.54
1090.363
110.315
1100.281
1110.968
1120.096
1130.95
1140.179
1150.156
1160.705
1170.443
1180.778
1190.451
120.579
1200.431
1210.733
1220.502
1230.239
1240.704
1250.995
1260.649
1270.215
1280.0161
1290.377
130.147
1300.216
1310.593
1320.199
1330.917
1340.555
1350.377
1360.587
1370.82
1380.0845
1390.453
140.726
1400.503
1410.529
1420.932
1430.438
1440.984
1450.404
1460.291
1470.204
1480.436
1490.00548
150.673
1500.49
1510.17
1520.0584
1530.586
1540.979
1550.631
1560.808
1570.767
1580.548
1590.703
160.173
1600.0715
1610.998
1620.22
1630.749
1640.173
1650.855
1660.658
1670.209
1680.411
1690.0197
170.254
180.605
190.0406
20.0244
200.0561
210.624
220.0851
230.109
240.742
250.725
260.814
270.0545
280.455
290.689
30.431
300.0531
310.343
320.01
330.8
340.146
350.844
360.0849
370.768
380.506
390.431
40.0115
400.761
410.447
420.749
430.78
440.143
450.235
460.385
470.592
480.447
490.683
50.479
500.715
510.403
520.256
530.925
540.281
550.0265
560.531
570.674
580.933
590.0721
60.972
600.373
610.955
620.734
630.282
640.743
650.213
668.05369e-7
670.416
680.342
690.168
70.81
700.267
710.923
720.381
730.124
740.464
750.888
760.343
770.00207
780.578
790.0471
80.169
800.318
810.442
820.13
830.771
840.42
850.0423
860.57
870.804
880.795
890.00312
90.228
900.771
910.125
920.217
930.842
940.345
950.84
960.905
970.453
980.108
990.00918



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: CNhs11049


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)
0000081 (blood cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000988 (hematopoietic cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000087 (inner cell mass)
0000091 (bilaminar disc)
0000178 (blood)
0000179 (haemolymphatic fluid)
0000358 (blastocyst)
0000463 (organism substance)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000478 (extraembryonic structure)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001009 (circulatory system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002331 (umbilical cord)
0002390 (hematopoietic system)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0004120 (mesoderm-derived structure)
0004535 (cardiovascular system)
0005423 (developing anatomical structure)
0005728 (extraembryonic mesoderm)
0007806 (connecting stalk)
0008780 (inner cell mass derived epiblast)

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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