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FF:10007-101B4: 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 16:11, 29 March 2012


Name:Universal RNA - Human Normal Tissues Biochain, pool1
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 stage34-76 years old adult
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberB208251
catalog numberCat:R4234565-1
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-penis0.00206
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.0391
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
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-endometrioid0.244
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0.0391
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: CNhs10612

Jaspar motifP-value
MA0002.20.0588
MA0003.10.0302
MA0004.10.464
MA0006.10.0461
MA0007.10.0969
MA0009.10.208
MA0014.10.553
MA0017.15.89941e-21
MA0018.20.248
MA0019.10.247
MA0024.10.0197
MA0025.10.0172
MA0027.10.731
MA0028.12.59179e-5
MA0029.10.829
MA0030.11.33758e-9
MA0031.12.73965e-9
MA0035.20.00391
MA0038.10.152
MA0039.20.0353
MA0040.10.159
MA0041.10.409
MA0042.10.437
MA0043.10.457
MA0046.12.14936e-78
MA0047.21.52211e-12
MA0048.10.0385
MA0050.10.0824
MA0051.10.333
MA0052.10.939
MA0055.10.0795
MA0057.10.713
MA0058.10.463
MA0059.10.115
MA0060.10.498
MA0061.16.74888e-4
MA0062.24.39529e-8
MA0065.27.05442e-6
MA0066.10.694
MA0067.10.0349
MA0068.10.00133
MA0069.10.511
MA0070.10.3
MA0071.10.714
MA0072.10.29
MA0073.10.812
MA0074.10.958
MA0076.16.83567e-6
MA0077.10.32
MA0078.10.0556
MA0079.20.127
MA0080.20.669
MA0081.10.0917
MA0083.10.575
MA0084.10.685
MA0087.10.2
MA0088.10.235
MA0090.10.00757
MA0091.10.726
MA0092.10.641
MA0093.10.468
MA0099.28.43269e-15
MA0100.10.182
MA0101.10.00167
MA0102.20.0558
MA0103.10.0779
MA0104.20.00651
MA0105.11.61721e-4
MA0106.10.573
MA0107.10.00163
MA0108.23.44803e-16
MA0111.10.96
MA0112.20.0343
MA0113.10.00838
MA0114.14.82534e-24
MA0115.17.30547e-6
MA0116.10.566
MA0117.10.316
MA0119.10.447
MA0122.10.605
MA0124.10.18
MA0125.10.16
MA0131.10.389
MA0135.10.38
MA0136.10.103
MA0137.27.2074e-6
MA0138.20.585
MA0139.10.881
MA0140.10.257
MA0141.10.0119
MA0142.10.779
MA0143.10.788
MA0144.12.64881e-4
MA0145.10.0146
MA0146.10.429
MA0147.10.00149
MA0148.16.72546e-9
MA0149.10.0307
MA0150.10.0153
MA0152.10.0039
MA0153.15.52268e-43
MA0154.10.524
MA0155.10.29
MA0156.10.0503
MA0157.19.36206e-4
MA0159.10.00895
MA0160.10.0401
MA0162.10.688
MA0163.10.0297
MA0164.10.194
MA0258.10.126
MA0259.10.0135



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: CNhs10612

Novel motifP-value
10.539
100.129
1000.876
1010.777
1020.0109
1030.738
1040.927
1050.721
1060.247
1070.0347
1080.775
1090.713
110.794
1100.641
1110.0195
1120.332
1130.072
1140.413
1150.72
1160.588
1170.0817
1180.734
1190.427
120.527
1200.414
1210.667
1220.953
1230.269
1240.504
1250.0891
1260.19
1270.00971
1280.737
1290.986
130.596
1300.551
1310.0799
1320.281
1330.425
1340.211
1350.18
1360.57
1370.598
1380.578
1390.332
140.468
1400.519
1410.677
1420.811
1430.00106
1440.071
1450.458
1460.0373
1470.939
1480.937
1490.487
150.501
1500.779
1510.599
1520.111
1530.844
1540.203
1550.63
1560.522
1570.793
1580.281
1590.495
160.621
1600.663
1610.839
1620.91
1630.929
1640.235
1650.0147
1660.622
1670.076
1680.461
1690.109
170.85
180.0112
190.0228
20.039
200.196
210.321
220.142
230.0868
240.84
250.585
260.678
270.569
280.746
290.0705
30.818
300.0294
310.733
320.606
330.634
340.178
350.411
360.125
370.729
380.636
390.103
40.0406
400.98
410.0281
420.838
430.994
440.553
450.0431
460.534
470.632
480.868
490.994
50.84
500.324
510.853
520.0656
530.775
540.742
550.794
560.711
570.16
580.657
590.441
60.371
600.234
610.453
620.938
630.485
640.673
650.499
660.0883
670.102
680.284
690.296
70.487
700.309
710.477
720.405
730.618
740.358
750.0665
760.00906
770.00629
780.593
790.4
80.949
800.136
810.336
820.99
830.752
840.754
850.497
860.965
870.356
880.421
890.686
90.37
900.493
910.547
920.762
930.942
940.0952
950.237
960.968
970.239
980.431
990.19



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: CNhs10612


FANTOM5 (FF) ontology

Direct parent terms

has_quality relathionship
PATO:0000461

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

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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