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FF:10053-101G8: 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 16:51, 29 March 2012


Name:blood, adult, pool1
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 stage18-47 years old adult
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyClontech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number9090107A
catalog numberCat:636592
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-penis0.315
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-Whole0.531
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: CNhs11761

Jaspar motifP-value
MA0002.21.92241e-7
MA0003.10.0781
MA0004.10.667
MA0006.10.532
MA0007.10.409
MA0009.10.0991
MA0014.10.675
MA0017.10.0216
MA0018.20.203
MA0019.10.488
MA0024.10.0198
MA0025.10.296
MA0027.10.653
MA0028.10.0487
MA0029.10.523
MA0030.10.681
MA0031.10.166
MA0035.22.13604e-4
MA0038.10.00155
MA0039.20.871
MA0040.10.869
MA0041.10.938
MA0042.10.753
MA0043.10.327
MA0046.10.447
MA0047.20.628
MA0048.10.246
MA0050.19.86178e-7
MA0051.10.0126
MA0052.10.208
MA0055.10.0609
MA0057.10.71
MA0058.10.532
MA0059.10.973
MA0060.11.06115e-4
MA0061.10.0863
MA0062.20.579
MA0065.20.00577
MA0066.10.0868
MA0067.10.97
MA0068.10.409
MA0069.10.676
MA0070.10.00767
MA0071.10.243
MA0072.10.735
MA0073.10.305
MA0074.10.389
MA0076.10.0503
MA0077.10.21
MA0078.10.509
MA0079.20.519
MA0080.29.5595e-16
MA0081.10.013
MA0083.10.704
MA0084.10.22
MA0087.10.595
MA0088.10.985
MA0090.10.0605
MA0091.10.159
MA0092.10.485
MA0093.10.49
MA0099.20.395
MA0100.10.508
MA0101.10.987
MA0102.20.00601
MA0103.10.12
MA0104.20.681
MA0105.16.36607e-5
MA0106.10.567
MA0107.10.974
MA0108.20.00795
MA0111.10.287
MA0112.20.00107
MA0113.10.885
MA0114.10.183
MA0115.10.632
MA0116.16.85802e-6
MA0117.10.946
MA0119.10.398
MA0122.10.613
MA0124.10.123
MA0125.10.0965
MA0131.10.217
MA0135.10.683
MA0136.17.77053e-12
MA0137.20.126
MA0138.20.329
MA0139.10.344
MA0140.11.40007e-12
MA0141.10.295
MA0142.10.582
MA0143.10.739
MA0144.10.85
MA0145.10.0867
MA0146.10.0314
MA0147.10.818
MA0148.10.885
MA0149.10.268
MA0150.10.0164
MA0152.10.0686
MA0153.10.101
MA0154.10.00379
MA0155.10.504
MA0156.13.56996e-4
MA0157.10.0902
MA0159.10.0229
MA0160.10.407
MA0162.10.158
MA0163.12.74592e-7
MA0164.10.845
MA0258.10.00535
MA0259.10.422



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: CNhs11761

Novel motifP-value
10.103
100.0726
1000.92
1010.256
1020.707
1030.103
1040.953
1050.0977
1060.00204
1070.18
1080.946
1090.128
110.0595
1100.606
1110.238
1120.0968
1130.174
1140.0428
1150.439
1160.504
1170.0839
1180.705
1190.255
120.619
1200.657
1210.498
1220.514
1230.0101
1240.109
1250.0235
1260.359
1270.17
1280.025
1290.582
130.61
1300.334
1310.969
1320.647
1330.328
1340.857
1350.458
1360.79
1370.101
1380.0717
1390.0131
140.335
1400.0419
1410.481
1420.931
1434.71449e-4
1440.625
1450.232
1460.735
1470.431
1480.082
1490.349
150.0735
1500.567
1510.19
1520.0805
1530.465
1540.505
1550.147
1560.466
1570.512
1580.281
1590.0502
160.278
1600.266
1610.301
1620.886
1630.0978
1640.284
1650.335
1660.565
1670.214
1680.197
1690.0177
170.254
180.113
190.212
20.365
200.656
210.596
220.292
230.0899
240.177
250.333
260.132
270.1
280.755
290.516
30.151
300.838
310.337
320.528
330.641
340.219
350.148
360.203
370.15
380.336
390.896
40.999
400.253
410.126
420.358
430.116
440.176
450.465
460.0862
470.188
480.239
490.0828
50.255
500.937
510.312
520.348
530.243
540.256
550.122
560.352
570.349
580.0837
590.0715
60.854
600.0424
610.314
620.0186
630.334
640.234
650.158
660.59
670.158
680.123
690.2
70.253
700.0668
710.126
720.385
730.225
740.478
750.0836
760.594
770.458
780.166
790.94
80.16
800.183
810.187
820.011
830.942
840.449
850.0181
860.13
870.486
880.994
890.422
90.424
900.0188
910.178
920.0268
930.704
940.197
950.495
960.0782
970.823
980.117
990.531



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: CNhs11761


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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