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FF:11661-122F5: 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 17:11, 29 March 2012


Name:Astrocyte - cerebellum, donor3
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 numberlot:5852
catalog numberSC1815
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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-4.829898e-4
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-0.199
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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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: CNhs12117

Jaspar motifP-value
MA0002.20.197
MA0003.10.511
MA0004.10.46
MA0006.10.291
MA0007.10.794
MA0009.10.0721
MA0014.10.242
MA0017.10.541
MA0018.20.21
MA0019.10.162
MA0024.10.583
MA0025.10.983
MA0027.10.966
MA0028.12.44983e-4
MA0029.10.983
MA0030.10.287
MA0031.10.0482
MA0035.20.749
MA0038.12.29757e-5
MA0039.20.654
MA0040.10.332
MA0041.10.434
MA0042.10.898
MA0043.10.00258
MA0046.10.05
MA0047.20.12
MA0048.10.15
MA0050.11.463e-6
MA0051.14.39332e-5
MA0052.10.557
MA0055.10.265
MA0057.10.95
MA0058.10.221
MA0059.10.336
MA0060.16.06544e-7
MA0061.10.117
MA0062.22.65812e-10
MA0065.20.431
MA0066.10.752
MA0067.10.012
MA0068.10.0127
MA0069.10.479
MA0070.10.0106
MA0071.10.993
MA0072.10.914
MA0073.10.851
MA0074.10.891
MA0076.11.33538e-5
MA0077.10.0783
MA0078.10.529
MA0079.20.905
MA0080.25.35078e-10
MA0081.10.00215
MA0083.14.15917e-4
MA0084.10.976
MA0087.10.992
MA0088.10.0964
MA0090.10.0584
MA0091.10.369
MA0092.11
MA0093.10.376
MA0099.20.00548
MA0100.10.182
MA0101.10.0398
MA0102.23.73349e-4
MA0103.10.448
MA0104.20.0735
MA0105.10.0442
MA0106.10.804
MA0107.10.167
MA0108.22.07574e-8
MA0111.10.248
MA0112.20.632
MA0113.10.204
MA0114.10.583
MA0115.10.39
MA0116.10.0287
MA0117.10.22
MA0119.10.829
MA0122.10.991
MA0124.10.495
MA0125.10.301
MA0131.10.5
MA0135.10.00806
MA0136.14.04914e-14
MA0137.20.148
MA0138.20.346
MA0139.10.4
MA0140.10.959
MA0141.10.395
MA0142.10.0888
MA0143.10.0934
MA0144.10.234
MA0145.10.63
MA0146.10.404
MA0147.10.097
MA0148.10.182
MA0149.10.0483
MA0150.19.7064e-4
MA0152.10.924
MA0153.10.206
MA0154.10.294
MA0155.10.0183
MA0156.11.23304e-12
MA0157.10.116
MA0159.10.208
MA0160.10.561
MA0162.10.259
MA0163.10.0573
MA0164.10.806
MA0258.10.367
MA0259.10.242



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: CNhs12117

Novel motifP-value
10.0395
100.00896
1000.825
1010.283
1020.206
1030.0791
1040.443
1050.0844
1060.508
1070.00617
1080.773
1090.53
110.924
1100.95
1110.0455
1120.218
1130.314
1140.0403
1150.427
1160.103
1170.0581
1180.166
1190.638
120.719
1200.572
1210.639
1220.927
1230.0196
1240.833
1250.398
1260.591
1270.586
1280.273
1290.637
130.347
1300.132
1310.138
1320.339
1330.994
1340.231
1350.697
1360.827
1370.0113
1380.114
1390.106
140.891
1400.9
1410.167
1420.199
1430.925
1440.681
1450.434
1460.304
1470.433
1480.0634
1490.337
150.186
1500.42
1510.914
1520.463
1530.0281
1540.485
1550.031
1560.839
1570.435
1580.115
1590.798
160.925
1600.266
1610.562
1620.149
1630.463
1640.086
1650.113
1660.459
1670.308
1680.131
1690.341
170.938
180.652
190.249
20.696
200.62
210.333
220.589
230.74
240.437
250.318
260.715
270.801
280.182
290.24
30.144
300.0719
310.27
326.37039e-5
330.837
340.184
350.584
360.117
370.248
380.635
390.548
40.574
400.714
410.439
420.155
430.357
440.76
450.454
460.962
470.311
480.835
490.327
50.215
500.74
510.885
520.489
530.367
540.861
550.564
560.704
570.916
580.137
590.162
60.56
600.998
610.195
620.213
630.912
640.319
650.311
660.781
670.631
680.00322
690.205
70.453
700.803
710.14
720.284
730.867
740.324
750.0112
760.00304
770.269
780.0728
790.106
80.56
800.524
810.868
820.865
830.805
840.56
850.768
860.332
870.477
880.43
890.127
90.506
900.0157
910.751
920.376
930.163
940.758
950.149
960.283
970.981
980.71
990.0106



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: CNhs12117


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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