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FF:10012-101C3: 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 16:25, 29 March 2012


Name:brain, 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
tissuebrain
dev stage77,79,81 years old adult
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyAmbion
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number0910061 -3
catalog numberCat:AM6000 Lot:0910061 -3
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-ToTALLY-RNA-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-Neural0.285
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-penis0.171
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.312
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0.0385
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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: CNhs10617

Jaspar motifP-value
MA0002.20.0103
MA0003.10.372
MA0004.10.349
MA0006.10.408
MA0007.10.29
MA0009.10.161
MA0014.10.564
MA0017.10.00398
MA0018.20.177
MA0019.10.566
MA0024.10.914
MA0025.10.352
MA0027.10.642
MA0028.10.0336
MA0029.10.0407
MA0030.10.219
MA0031.10.971
MA0035.20.0293
MA0038.10.119
MA0039.20.11
MA0040.10.504
MA0041.10.23
MA0042.10.668
MA0043.10.894
MA0046.10.0224
MA0047.20.122
MA0048.10.0521
MA0050.10.00425
MA0051.10.129
MA0052.10.352
MA0055.12.00559e-4
MA0057.10.988
MA0058.10.301
MA0059.10.0701
MA0060.10.638
MA0061.10.00591
MA0062.20.00168
MA0065.20.00117
MA0066.10.0336
MA0067.10.798
MA0068.10.28
MA0069.10.543
MA0070.10.186
MA0071.10.0291
MA0072.10.38
MA0073.10.464
MA0074.10.277
MA0076.10.0695
MA0077.10.2
MA0078.10.928
MA0079.20.493
MA0080.27.3334e-8
MA0081.10.0276
MA0083.10.058
MA0084.10.809
MA0087.10.387
MA0088.10.0921
MA0090.10.237
MA0091.10.71
MA0092.10.419
MA0093.10.373
MA0099.27.17376e-14
MA0100.10.529
MA0101.10.00148
MA0102.20.145
MA0103.10.253
MA0104.20.363
MA0105.17.11063e-4
MA0106.10.0255
MA0107.10.00278
MA0108.20.495
MA0111.10.52
MA0112.20.00161
MA0113.10.405
MA0114.10.00357
MA0115.10.587
MA0116.10.00608
MA0117.10.905
MA0119.10.0379
MA0122.10.793
MA0124.10.799
MA0125.10.199
MA0131.10.646
MA0135.10.00628
MA0136.19.43862e-12
MA0137.20.743
MA0138.20.11
MA0139.10.458
MA0140.10.00659
MA0141.10.0197
MA0142.10.893
MA0143.10.41
MA0144.10.553
MA0145.10.278
MA0146.10.00732
MA0147.10.256
MA0148.10.121
MA0149.10.0141
MA0150.15.42885e-4
MA0152.10.865
MA0153.10.175
MA0154.10.0683
MA0155.10.785
MA0156.13.688e-7
MA0157.10.754
MA0159.10.00868
MA0160.10.0362
MA0162.10.142
MA0163.14.56859e-6
MA0164.10.715
MA0258.10.0122
MA0259.10.714



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: CNhs10617

Novel motifP-value
10.0429
100.0284
1000.236
1010.806
1020.731
1030.283
1040.139
1050.147
1060.0801
1070.18
1080.903
1090.00779
110.0135
1100.0327
1110.0633
1120.525
1130.662
1140.123
1150.583
1160.208
1170.00796
1180.0985
1190.126
120.524
1200.188
1210.445
1220.697
1230.26
1240.0427
1250.277
1260.0393
1270.545
1280.272
1290.524
134.20359e-4
1300.371
1310.0408
1320.681
1330.00144
1340.386
1350.0754
1360.00548
1370.865
1380.827
1390.12
140.782
1400.138
1410.377
1420.82
1430.0144
1440.962
1450.0805
1460.55
1470.902
1480.457
1490.471
150.0581
1500.135
1510.68
1520.135
1530.824
1540.589
1550.448
1560.36
1570.439
1580.924
1590.0935
160.0858
1600.281
1610.18
1620.773
1630.708
1640.0141
1650.0747
1660.922
1670.415
1680.629
1690.0102
170.17
180.282
190.252
20.913
200.0592
210.0566
220.277
230.533
240.0958
250.466
265.73358e-5
270.885
280.595
290.00891
30.0279
300.57
310.988
320.0589
330.0632
340.836
350.588
360.118
370.0349
380.33
390.298
40.794
400.0403
410.435
420.154
430.118
440.283
450.822
460.061
470.0673
480.049
490.125
50.563
500.304
510.553
520.746
530.898
540.493
550.444
560.48
570.192
580.304
590.208
60.666
600.0956
610.0637
620.203
630.16
640.204
650.326
660.175
670.343
680.237
690.547
70.0447
700.0388
710.00707
720.511
730.0362
740.762
750.025
760.263
770.262
780.00168
790.434
80.0746
800.914
810.67
820.6
830.248
840.505
850.295
860.202
870.00542
880.828
890.699
90.539
900.0749
910.558
920.574
930.973
940.0916
950.0176
960.938
970.712
980.202
990.918



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: CNhs10617


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
0000033 (head)
0000061 (anatomical structure)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004121 (ectoderm-derived structure)
0005423 (developing anatomical structure)
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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