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FF:10083-102B2: 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 16:54, 29 March 2012


Name:cerebellum, 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
tissuecerebellum
dev stage22-68 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 number8101369A-3
catalog numberCat: 636643 Lot: 8101369A-3
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-Neural0.202
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-penis0.451
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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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
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: CNhs11795

Jaspar motifP-value
MA0002.20.00447
MA0003.10.186
MA0004.10.316
MA0006.10.294
MA0007.10.331
MA0009.10.491
MA0014.10.576
MA0017.10.0052
MA0018.20.0487
MA0019.10.83
MA0024.10.618
MA0025.10.355
MA0027.10.884
MA0028.10.0697
MA0029.10.115
MA0030.10.469
MA0031.10.952
MA0035.20.027
MA0038.10.369
MA0039.20.149
MA0040.10.928
MA0041.10.523
MA0042.10.892
MA0043.10.623
MA0046.10.0503
MA0047.20.0048
MA0048.10.298
MA0050.10.00121
MA0051.10.0128
MA0052.10.403
MA0055.10.0386
MA0057.10.549
MA0058.10.305
MA0059.10.0735
MA0060.10.185
MA0061.10.00357
MA0062.20.00169
MA0065.20.00248
MA0066.10.0448
MA0067.10.483
MA0068.10.845
MA0069.10.966
MA0070.10.406
MA0071.10.209
MA0072.10.956
MA0073.10.268
MA0074.10.281
MA0076.10.0977
MA0077.10.345
MA0078.10.884
MA0079.20.726
MA0080.22.9334e-9
MA0081.10.0382
MA0083.10.00766
MA0084.10.87
MA0087.10.858
MA0088.10.206
MA0090.10.0772
MA0091.10.96
MA0092.10.359
MA0093.10.37
MA0099.26.25093e-20
MA0100.10.399
MA0101.14.27626e-4
MA0102.20.034
MA0103.10.684
MA0104.20.569
MA0105.16.62643e-4
MA0106.10.00924
MA0107.16.94773e-4
MA0108.20.581
MA0111.10.434
MA0112.20.00219
MA0113.10.274
MA0114.10.00794
MA0115.10.934
MA0116.10.00417
MA0117.10.786
MA0119.10.101
MA0122.10.368
MA0124.10.955
MA0125.10.386
MA0131.10.852
MA0135.10.0588
MA0136.11.45606e-14
MA0137.20.925
MA0138.20.107
MA0139.10.597
MA0140.10.00246
MA0141.10.0408
MA0142.10.767
MA0143.10.86
MA0144.10.314
MA0145.10.159
MA0146.10.0539
MA0147.10.396
MA0148.10.0105
MA0149.10.025
MA0150.18.57841e-5
MA0152.10.702
MA0153.10.182
MA0154.10.0273
MA0155.10.407
MA0156.11.45148e-9
MA0157.10.467
MA0159.10.00637
MA0160.10.0919
MA0162.10.133
MA0163.11.84613e-5
MA0164.10.952
MA0258.10.0345
MA0259.10.873



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: CNhs11795

Novel motifP-value
10.0783
100.0633
1000.509
1010.964
1020.509
1030.0293
1040.0792
1050.0893
1060.0299
1070.0793
1080.8
1090.00475
110.0196
1100.0602
1110.395
1120.635
1130.364
1140.194
1150.61
1160.352
1170.0109
1180.249
1190.424
120.579
1200.118
1210.655
1220.599
1230.429
1240.323
1250.802
1260.0264
1270.499
1280.363
1290.497
130.00157
1300.0549
1310.435
1320.52
1330.0433
1340.533
1350.622
1360.00847
1370.479
1380.887
1390.228
140.624
1400.452
1410.666
1420.882
1430.0313
1440.99
1450.23
1460.336
1470.916
1480.0508
1490.161
150.0541
1500.204
1510.729
1520.0541
1530.797
1540.606
1550.649
1560.74
1570.269
1580.176
1590.0204
160.0862
1600.217
1610.293
1620.934
1630.566
1640.0372
1650.0435
1660.709
1670.932
1680.355
1690.0239
170.0825
180.181
190.302
20.848
200.24
210.101
220.244
230.17
240.0235
250.46
266.39698e-4
270.714
280.591
290.0149
30.0373
300.977
310.997
320.115
330.045
340.613
350.784
360.152
370.0498
380.352
390.194
40.946
400.0526
410.279
420.164
430.0914
440.415
450.689
460.0617
470.0603
480.0802
490.22
50.477
500.331
510.406
520.436
530.929
540.434
550.58
560.312
570.384
580.347
590.0678
60.928
600.0419
610.0672
620.151
630.128
640.34
650.31
660.152
670.316
680.167
690.576
70.0369
700.0165
710.0089
720.225
730.0317
740.855
750.0406
760.455
770.17
780.0156
790.408
80.0467
800.137
810.575
820.73
830.027
840.786
850.213
860.225
878.05916e-4
880.85
890.318
90.316
900.184
910.783
920.429
930.611
940.145
950.0257
960.702
970.586
980.391
990.507



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: CNhs11795


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
0000025 (tube)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
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)
0000477 (anatomical cluster)
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)
0001049 (neural tube)
0001062 (anatomical entity)
0001895 (metencephalon)
0002028 (hindbrain)
0002037 (cerebellum)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002680 (regional part of metencephalon)
0003057 (chordal neural plate)
0003075 (neural plate)
0003076 (posterior neural tube)
0004121 (ectoderm-derived structure)
0004732 (segmental subdivision of nervous system)
0004733 (segmental subdivision of hindbrain)
0005068 (neural rod)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007023 (adult organism)
0007135 (neural keel)
0007284 (presumptive neural plate)

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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