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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:0000144,CL:0000255,CL:0000548,CL:0000988,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,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
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
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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: CNhs11050

Jaspar motifP-value
MA0002.20.219
MA0003.10.557
MA0004.10.44
MA0006.10.12
MA0007.10.113
MA0009.10.715
MA0014.10.247
MA0017.10.941
MA0018.21.18543e-5
MA0019.10.918
MA0024.14.03536e-8
MA0025.10.911
MA0027.10.567
MA0028.14.21054e-5
MA0029.10.716
MA0030.10.0441
MA0031.10.0608
MA0035.20.0682
MA0038.10.00864
MA0039.20.107
MA0040.10.0202
MA0041.10.165
MA0042.10.201
MA0043.10.0865
MA0046.10.154
MA0047.20.717
MA0048.10.0976
MA0050.10.00304
MA0051.10.0118
MA0052.10.00931
MA0055.10.0234
MA0057.10.425
MA0058.10.331
MA0059.10.0692
MA0060.11.28919e-10
MA0061.11.04911e-14
MA0062.23.0252e-7
MA0065.20.465
MA0066.10.11
MA0067.10.79
MA0068.10.209
MA0069.10.617
MA0070.10.414
MA0071.10.657
MA0072.10.601
MA0073.10.55
MA0074.10.844
MA0076.14.45981e-6
MA0077.10.745
MA0078.10.0917
MA0079.20.28
MA0080.20.84
MA0081.10.787
MA0083.10.671
MA0084.10.761
MA0087.10.205
MA0088.10.108
MA0090.13.6897e-5
MA0091.10.013
MA0092.10.217
MA0093.10.305
MA0099.20.00113
MA0100.10.122
MA0101.11.01006e-17
MA0102.20.611
MA0103.10.228
MA0104.28.34751e-4
MA0105.11.03043e-4
MA0106.10.0405
MA0107.19.54707e-23
MA0108.20.00611
MA0111.10.889
MA0112.20.0203
MA0113.10.0629
MA0114.10.402
MA0115.10.346
MA0116.10.996
MA0117.10.0355
MA0119.10.103
MA0122.10.256
MA0124.10.399
MA0125.10.202
MA0131.10.0526
MA0135.10.0197
MA0136.10.146
MA0137.20.0051
MA0138.20.133
MA0139.10.974
MA0140.10.115
MA0141.10.601
MA0142.10.304
MA0143.10.0286
MA0144.10.955
MA0145.10.00198
MA0146.10.354
MA0147.10.0013
MA0148.10.87
MA0149.10.328
MA0150.10.201
MA0152.10.217
MA0153.11.85353e-4
MA0154.10.714
MA0155.10.204
MA0156.10.035
MA0157.10.105
MA0159.10.53
MA0160.10.0427
MA0162.10.0404
MA0163.10.197
MA0164.10.748
MA0258.10.239
MA0259.10.13



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: CNhs11050

Novel motifP-value
10.974
100.135
1000.183
1010.216
1020.954
1030.43
1040.752
1050.536
1060.0409
1070.0289
1080.492
1090.978
110.606
1100.177
1110.474
1120.617
1130.7
1140.237
1150.629
1160.45
1170.51
1180.423
1190.433
120.52
1200.978
1210.893
1220.276
1230.152
1240.373
1250.602
1260.935
1270.977
1280.0258
1290.393
130.215
1300.791
1310.489
1320.396
1330.975
1340.301
1350.812
1360.465
1370.503
1380.153
1390.555
140.792
1400.324
1410.245
1420.991
1430.99
1440.494
1450.434
1460.291
1470.131
1480.222
1490.00691
150.708
1500.465
1510.319
1520.0794
1530.209
1540.788
1550.403
1560.681
1570.938
1580.998
1590.485
160.281
1600.35
1610.54
1620.153
1630.56
1640.711
1650.84
1660.81
1670.142
1680.549
1690.0292
170.339
180.731
190.0241
20.119
200.146
210.0244
220.0687
230.0171
240.221
250.55
260.682
270.285
280.63
290.487
30.588
300.0306
310.251
320.0319
330.861
340.226
350.789
360.0649
370.641
380.512
390.155
40.194
400.959
410.23
420.464
430.437
440.957
450.0705
460.595
470.955
480.859
490.706
50.162
500.731
510.625
520.0993
530.662
540.226
556.232e-4
560.792
570.971
580.709
590.148
60.974
600.234
610.58
620.965
630.385
640.692
650.246
660.0365
670.161
680.122
690.0524
70.748
700.123
710.495
720.271
730.123
740.494
750.769
760.268
770.00413
780.32
790.0223
80.489
800.377
810.571
820.106
830.262
840.358
850.0208
860.787
870.351
880.455
890.0224
90.18
900.886
910.478
920.234
930.634
940.979
950.467
960.797
970.0419
980.138
990.115



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: CNhs11050


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)
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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