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FF:11316-117D2: 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 17:03, 29 March 2012


Name:Astrocyte - cerebral cortex, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuecerebral cortex
dev stagefetus
sexunknown
agefetal
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 number1091
catalog numberSC1805
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-penis0.051
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-lymphoma0.62
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
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs11960

Jaspar motifP-value
MA0002.20.00144
MA0003.10.0553
MA0004.10.138
MA0006.10.617
MA0007.10.323
MA0009.10.175
MA0014.10.691
MA0017.10.00203
MA0018.20.899
MA0019.10.95
MA0024.11.1598e-5
MA0025.10.26
MA0027.10.152
MA0028.10.547
MA0029.10.298
MA0030.10.0432
MA0031.10.00163
MA0035.20.0415
MA0038.12.09924e-4
MA0039.20.69
MA0040.10.0545
MA0041.10.185
MA0042.10.134
MA0043.10.188
MA0046.10.655
MA0047.22.49518e-6
MA0048.10.13
MA0050.10.00248
MA0051.10.0269
MA0052.10.00329
MA0055.10.364
MA0057.10.41
MA0058.10.0622
MA0059.10.0713
MA0060.12.22923e-12
MA0061.10.00373
MA0062.20.307
MA0065.20.00203
MA0066.10.101
MA0067.10.274
MA0068.13.44487e-4
MA0069.10.888
MA0070.10.0362
MA0071.10.179
MA0072.10.195
MA0073.10.962
MA0074.10.556
MA0076.10.538
MA0077.10.0521
MA0078.10.899
MA0079.20.646
MA0080.23.73574e-15
MA0081.10.0394
MA0083.10.665
MA0084.10.938
MA0087.10.478
MA0088.10.389
MA0090.10.54
MA0091.10.00781
MA0092.10.329
MA0093.10.141
MA0099.22.16226e-5
MA0100.10.432
MA0101.10.0293
MA0102.20.00552
MA0103.10.038
MA0104.20.134
MA0105.11.04805e-4
MA0106.10.121
MA0107.10.00631
MA0108.20.774
MA0111.10.617
MA0112.23.71629e-5
MA0113.10.136
MA0114.10.0381
MA0115.10.875
MA0116.16.7773e-4
MA0117.10.663
MA0119.10.373
MA0122.10.679
MA0124.10.742
MA0125.10.0249
MA0131.10.552
MA0135.10.532
MA0136.11.17798e-14
MA0137.20.167
MA0138.20.18
MA0139.10.0876
MA0140.10.024
MA0141.10.0654
MA0142.10.00376
MA0143.10.0654
MA0144.10.0404
MA0145.10.198
MA0146.10.147
MA0147.10.125
MA0148.12.04088e-4
MA0149.10.0318
MA0150.10.00145
MA0152.10.203
MA0153.10.765
MA0154.10.00258
MA0155.10.392
MA0156.11.77455e-6
MA0157.10.00402
MA0159.10.00632
MA0160.10.0233
MA0162.10.556
MA0163.11.84847e-6
MA0164.10.88
MA0258.10.00725
MA0259.10.51



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: CNhs11960

Novel motifP-value
10.0953
100.15
1000.938
1010.726
1020.763
1030.106
1040.501
1050.504
1060.0327
1070.756
1080.479
1090.0212
110.0774
1100.278
1110.0569
1120.0178
1130.209
1140.00601
1150.504
1160.928
1170.207
1180.336
1190.213
120.536
1200.863
1210.804
1220.25
1230.543
1240.283
1250.89
1260.14
1270.112
1280.308
1290.124
130.321
1300.154
1310.8
1320.842
1330.701
1340.868
1350.0192
1360.847
1370.155
1380.0614
1390.00269
140.757
1400.313
1410.209
1420.811
1430.00401
1440.906
1450.699
1460.609
1470.872
1480.0987
1490.0953
150.101
1500.532
1510.262
1520.0865
1530.304
1540.736
1550.178
1560.523
1570.154
1580.086
1590.608
160.266
1600.251
1610.811
1620.585
1630.514
1640.0652
1650.369
1660.407
1670.854
1680.473
1690.00796
170.0921
180.0939
190.368
20.424
200.829
210.797
220.202
230.0542
240.527
250.451
260.531
270.152
280.868
290.253
30.0994
300.793
310.638
320.0837
330.533
340.553
350.313
360.0904
370.0438
380.186
390.851
40.605
400.165
410.186
420.279
430.102
440.471
450.406
460.1
470.215
480.26
490.0964
50.108
500.654
510.26
520.505
530.48
540.237
550.211
560.507
570.534
580.101
590.0866
60.944
600.0761
610.215
620.0642
630.216
640.433
650.0598
660.522
670.721
680.229
690.996
70.34
700.0147
710.0705
720.186
730.0622
740.679
750.0486
760.419
770.152
780.33
790.249
80.268
800.187
810.464
820.0181
830.934
840.437
850.0201
860.218
870.924
880.858
890.142
90.21
900.305
910.879
920.0254
930.014
940.0519
950.0637
960.172
970.519
980.243
990.708



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: CNhs11960


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)
0002605 (astrocyte of the cerebral cortex)

UBERON: Anatomy
0000025 (tube)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
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)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0000956 (cerebral cortex)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001869 (cerebral hemisphere)
0001890 (forebrain)
0001893 (telencephalon)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005291 (embryonic tissue)
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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