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FF:12181-129A3: 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 17:02, 29 March 2012


Name:Whole blood (ribopure), donor090309, donation3
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 typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationMatched_genome_OSC(contact:Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
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-penis0.158
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.33
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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-Whole0.196
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-Whole0.433
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: CNhs11948

Jaspar motifP-value
MA0002.21.38341e-9
MA0003.10.0755
MA0004.10.44
MA0006.10.455
MA0007.10.778
MA0009.10.0472
MA0014.10.723
MA0017.10.0875
MA0018.20.00646
MA0019.10.304
MA0024.10.00738
MA0025.10.393
MA0027.10.724
MA0028.10.757
MA0029.10.662
MA0030.10.108
MA0031.12.48723e-4
MA0035.28.82658e-5
MA0038.10.00299
MA0039.20.404
MA0040.10.542
MA0041.10.767
MA0042.10.732
MA0043.10.444
MA0046.10.282
MA0047.20.343
MA0048.10.222
MA0050.13.93205e-6
MA0051.10.0613
MA0052.10.00905
MA0055.10.0286
MA0057.10.907
MA0058.10.436
MA0059.10.458
MA0060.14.05596e-6
MA0061.10.0999
MA0062.20.0127
MA0065.20.141
MA0066.10.279
MA0067.10.521
MA0068.10.966
MA0069.10.551
MA0070.10.0135
MA0071.10.564
MA0072.10.53
MA0073.10.436
MA0074.10.804
MA0076.10.833
MA0077.10.286
MA0078.10.908
MA0079.20.813
MA0080.29.59064e-18
MA0081.10.00515
MA0083.10.638
MA0084.10.868
MA0087.10.748
MA0088.10.416
MA0090.10.011
MA0091.10.168
MA0092.10.846
MA0093.10.335
MA0099.20.107
MA0100.10.681
MA0101.10.987
MA0102.20.00468
MA0103.10.12
MA0104.20.276
MA0105.16.45333e-4
MA0106.10.484
MA0107.10.832
MA0108.21.02326e-6
MA0111.10.201
MA0112.20.00126
MA0113.10.487
MA0114.10.412
MA0115.10.774
MA0116.12.75115e-5
MA0117.10.675
MA0119.10.423
MA0122.10.953
MA0124.10.768
MA0125.10.0823
MA0131.10.538
MA0135.10.516
MA0136.11.40736e-20
MA0137.20.655
MA0138.20.352
MA0139.10.297
MA0140.11.83249e-12
MA0141.10.467
MA0142.10.898
MA0143.10.823
MA0144.10.256
MA0145.10.111
MA0146.10.00311
MA0147.10.264
MA0148.10.638
MA0149.10.419
MA0150.10.0683
MA0152.10.0282
MA0153.10.0331
MA0154.10.00629
MA0155.10.705
MA0156.11.97586e-12
MA0157.10.00331
MA0159.10.189
MA0160.10.653
MA0162.10.469
MA0163.11.70963e-5
MA0164.10.653
MA0258.10.0102
MA0259.10.198



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: CNhs11948

Novel motifP-value
10.134
100.0499
1000.643
1010.181
1020.504
1030.339
1040.717
1050.349
1060.0131
1070.429
1080.993
1090.133
110.0808
1100.347
1110.255
1120.0919
1130.169
1140.0444
1150.634
1160.604
1170.0323
1180.269
1190.33
120.361
1200.415
1210.953
1220.577
1230.00978
1240.267
1250.203
1260.547
1270.276
1280.0155
1290.614
130.95
1300.426
1310.974
1320.655
1330.859
1340.911
1350.415
1360.98
1370.0112
1380.048
1390.00933
140.161
1400.211
1410.43
1420.742
1430.00313
1440.614
1450.166
1460.968
1470.131
1480.0927
1490.472
150.0776
1500.747
1510.195
1520.194
1530.515
1540.74
1550.253
1560.756
1570.268
1580.471
1590.187
160.363
1600.453
1610.226
1620.861
1630.472
1640.183
1650.109
1660.86
1670.846
1680.237
1690.0136
170.375
180.558
190.226
20.207
200.663
210.187
220.217
230.107
240.049
250.32
260.141
270.102
280.536
290.507
30.0644
300.863
310.545
320.966
330.75
340.247
350.2
360.51
370.153
380.362
390.943
40.79
400.471
410.257
420.247
430.146
440.207
450.523
460.0785
470.154
480.263
490.105
50.339
500.88
510.389
520.454
530.098
540.265
550.0867
560.301
570.628
580.0845
590.0533
60.751
600.0635
610.275
620.0213
630.527
640.313
650.184
660.347
670.179
680.552
690.178
70.284
700.063
710.114
720.248
730.231
740.986
750.0904
760.433
770.495
780.328
790.567
80.294
800.121
810.224
820.0152
830.481
840.195
850.165
860.127
870.556
880.712
890.546
90.282
900.0174
910.32
920.0559
930.478
940.201
950.322
960.068
970.671
980.0297
990.661



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: CNhs11948


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

UBERON: Anatomy
0000061 (anatomical structure)
0000178 (blood)
0000179 (haemolymphatic fluid)
0000463 (organism substance)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0001009 (circulatory system)
0001062 (anatomical entity)
0002193 (hemolymphoid system)
0002390 (hematopoietic system)
0004535 (cardiovascular system)
0007023 (adult organism)

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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