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FF:11500-119F6: 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 16:44, 29 March 2012


Name:Astrocyte - cerebellum, donor1
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 stageNA
sexNA
ageNA
cell typeastrocyte
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberSC1815
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-penis-0.118
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-lymphoma0.245
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs11321

Jaspar motifP-value
MA0002.20.0655
MA0003.10.838
MA0004.10.302
MA0006.10.581
MA0007.10.945
MA0009.10.0394
MA0014.10.823
MA0017.10.186
MA0018.20.861
MA0019.10.156
MA0024.12.50585e-5
MA0025.10.935
MA0027.10.319
MA0028.10.971
MA0029.10.698
MA0030.10.381
MA0031.10.143
MA0035.20.899
MA0038.11.0379e-8
MA0039.20.423
MA0040.10.749
MA0041.10.333
MA0042.10.874
MA0043.10.165
MA0046.10.194
MA0047.20.0251
MA0048.10.178
MA0050.11.9097e-4
MA0051.10.0289
MA0052.10.389
MA0055.10.0436
MA0057.10.711
MA0058.10.311
MA0059.10.101
MA0060.18.92091e-20
MA0061.10.00539
MA0062.20.0678
MA0065.20.0102
MA0066.10.307
MA0067.10.0426
MA0068.10.0224
MA0069.10.626
MA0070.18.11554e-5
MA0071.10.51
MA0072.10.989
MA0073.10.875
MA0074.10.469
MA0076.10.871
MA0077.10.164
MA0078.10.97
MA0079.20.739
MA0080.24.23502e-10
MA0081.10.0693
MA0083.10.063
MA0084.10.978
MA0087.10.594
MA0088.10.251
MA0090.10.0841
MA0091.10.229
MA0092.10.458
MA0093.10.404
MA0099.20.209
MA0100.10.727
MA0101.10.126
MA0102.20.00149
MA0103.10.00503
MA0104.20.157
MA0105.11.31892e-4
MA0106.10.418
MA0107.10.0676
MA0108.25.72972e-7
MA0111.10.235
MA0112.20.0223
MA0113.10.941
MA0114.10.227
MA0115.10.875
MA0116.17.45301e-4
MA0117.10.392
MA0119.10.241
MA0122.10.767
MA0124.10.481
MA0125.10.0532
MA0131.10.939
MA0135.10.0138
MA0136.11.69349e-8
MA0137.20.675
MA0138.20.57
MA0139.10.382
MA0140.10.557
MA0141.10.395
MA0142.10.391
MA0143.10.256
MA0144.10.402
MA0145.10.664
MA0146.10.856
MA0147.10.14
MA0148.10.0297
MA0149.10.0284
MA0150.10.00189
MA0152.10.357
MA0153.10.116
MA0154.10.0355
MA0155.10.298
MA0156.16.10689e-4
MA0157.10.263
MA0159.10.0466
MA0160.10.339
MA0162.10.436
MA0163.11.40441e-4
MA0164.10.887
MA0258.10.0344
MA0259.10.451



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: CNhs11321

Novel motifP-value
10.00993
100.00792
1000.955
1010.441
1020.296
1030.175
1040.744
1050.131
1060.0291
1070.875
1080.181
1090.19
110.194
1100.765
1110.018
1120.0387
1130.546
1140.0096
1150.762
1160.812
1170.0255
1180.113
1190.0317
120.905
1200.967
1210.426
1220.916
1230.00119
1240.927
1250.288
1260.554
1270.222
1280.221
1290.456
130.544
1300.0233
1310.658
1320.91
1330.383
1340.227
1350.605
1360.894
1370.0595
1380.0511
1394.57678e-4
140.85
1400.0786
1410.384
1420.598
1430.285
1440.84
1450.548
1460.42
1470.98
1480.00804
1490.429
150.101
1500.83
1510.272
1520.276
1530.121
1540.306
1550.0159
1560.768
1570.77
1580.0696
1590.928
160.262
1600.853
1610.543
1620.775
1630.689
1640.0313
1650.129
1660.964
1670.238
1680.499
1690.545
170.207
180.243
190.925
20.974
200.646
210.285
220.835
230.221
240.635
250.477
260.429
270.728
280.446
290.131
30.0458
300.118
310.803
320.564
330.864
340.641
350.109
360.114
370.0293
380.384
390.73
40.818
400.685
410.295
420.225
430.123
440.183
450.967
460.197
470.234
480.355
490.092
50.177
500.676
510.562
520.621
530.299
540.407
550.587
560.752
570.418
580.0877
590.801
60.497
600.119
610.0752
620.0406
630.3
640.748
650.4
660.154
670.401
680.399
690.864
70.504
700.021
710.0602
720.284
730.057
740.497
750.0022
760.0173
770.711
780.0444
790.402
80.355
800.657
810.342
820.0448
830.847
840.564
850.0376
860.0893
870.912
880.516
890.799
90.832
900.00205
910.541
920.0493
930.306
940.255
950.0276
960.149
970.886
980.765
990.115



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: CNhs11321


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000030 (glioblast)
0000055 (non-terminally differentiated cell)
0000095 (neuron associated cell)
0000123 (neuron associated cell (sensu Vertebrata))
0000125 (glial cell)
0000126 (macroglial cell)
0000127 (astrocyte)
0000128 (oligodendrocyte)
0000133 (neurectodermal cell)
0000219 (motile cell)
0000221 (ectodermal cell)
0000243 (glial cell (sensu Vertebrata))
0000255 (eukaryotic cell)
0000333 (migratory neural crest cell)
0000339 (glioblast (sensu Vertebrata))
0000548 (animal cell)
0002319 (neural cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002453 (oligodendrocyte precursor cell)
0002603 (astrocyte of the cerebellum)

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)
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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