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FF:11392-118C6: 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 17:06, 29 March 2012


Name:Astrocyte - cerebral cortex, donor3
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 number3641
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-penis-0.015
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-lymphoma0.63
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
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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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: CNhs12005

Jaspar motifP-value
MA0002.24.55744e-4
MA0003.10.0869
MA0004.10.145
MA0006.10.696
MA0007.10.392
MA0009.10.177
MA0014.10.584
MA0017.10.00221
MA0018.20.441
MA0019.10.919
MA0024.12.85241e-6
MA0025.10.485
MA0027.10.428
MA0028.10.674
MA0029.10.714
MA0030.10.081
MA0031.10.0133
MA0035.20.0644
MA0038.12.43518e-6
MA0039.20.922
MA0040.10.0438
MA0041.10.281
MA0042.10.127
MA0043.10.842
MA0046.10.996
MA0047.28.17095e-4
MA0048.10.255
MA0050.10.00715
MA0051.10.0264
MA0052.10.517
MA0055.10.303
MA0057.10.482
MA0058.10.0771
MA0059.10.0642
MA0060.11.36246e-14
MA0061.10.0182
MA0062.20.384
MA0065.20.00231
MA0066.10.0691
MA0067.10.287
MA0068.10.00102
MA0069.10.973
MA0070.10.0184
MA0071.10.25
MA0072.10.366
MA0073.10.846
MA0074.10.486
MA0076.10.569
MA0077.10.0377
MA0078.10.709
MA0079.20.701
MA0080.22.39032e-14
MA0081.10.0344
MA0083.10.18
MA0084.10.438
MA0087.10.625
MA0088.10.452
MA0090.10.133
MA0091.10.0235
MA0092.10.485
MA0093.10.16
MA0099.21.90627e-7
MA0100.10.275
MA0101.10.196
MA0102.20.00572
MA0103.10.0428
MA0104.20.187
MA0105.12.72059e-5
MA0106.10.148
MA0107.10.0851
MA0108.20.0104
MA0111.10.465
MA0112.21.06548e-4
MA0113.10.21
MA0114.10.0259
MA0115.10.373
MA0116.13.41034e-4
MA0117.10.784
MA0119.10.311
MA0122.10.84
MA0124.10.546
MA0125.10.0137
MA0131.10.508
MA0135.10.483
MA0136.11.63296e-15
MA0137.20.372
MA0138.20.187
MA0139.10.0656
MA0140.10.0565
MA0141.10.0429
MA0142.10.0302
MA0143.10.0894
MA0144.10.0739
MA0145.10.244
MA0146.10.0847
MA0147.10.192
MA0148.10.00666
MA0149.10.0359
MA0150.19.02708e-4
MA0152.10.2
MA0153.10.781
MA0154.10.00295
MA0155.10.669
MA0156.11.21391e-5
MA0157.10.0168
MA0159.10.00894
MA0160.10.029
MA0162.10.507
MA0163.14.33028e-8
MA0164.10.604
MA0258.10.00621
MA0259.10.475



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: CNhs12005

Novel motifP-value
10.0608
100.0898
1000.899
1010.525
1020.64
1030.0985
1040.871
1050.256
1060.0478
1070.592
1080.5
1090.0278
110.0613
1100.162
1110.0405
1120.022
1130.439
1140.00213
1150.34
1160.893
1170.102
1180.375
1190.179
120.518
1200.977
1210.775
1220.325
1230.213
1240.345
1250.913
1260.179
1270.0804
1280.263
1290.246
130.277
1300.281
1310.449
1320.957
1330.981
1340.861
1350.242
1360.854
1370.158
1380.0612
1390.0019
140.765
1400.101
1410.249
1420.693
1430.00338
1440.807
1450.818
1460.9
1470.907
1480.0144
1490.12
150.0794
1500.569
1510.325
1520.172
1530.279
1540.95
1550.295
1560.519
1570.358
1580.109
1590.743
160.233
1600.214
1610.601
1620.936
1630.785
1640.0596
1650.142
1660.287
1670.623
1680.503
1690.00924
170.129
180.113
190.412
20.528
200.844
210.619
220.244
230.0714
240.352
250.463
260.369
270.188
280.761
290.133
30.0542
300.89
310.726
320.263
330.52
340.671
350.159
360.0401
370.0506
380.188
390.993
40.648
400.193
410.159
420.186
430.0858
440.343
450.538
460.0472
470.124
480.197
490.0966
50.122
500.781
510.312
520.524
530.6
540.338
550.215
560.458
570.474
580.0621
590.133
60.845
600.0629
610.333
620.0422
630.187
640.291
650.106
660.549
670.774
680.653
690.795
70.282
700.00651
710.0521
720.145
730.116
740.218
750.0463
760.344
770.149
780.211
790.546
80.273
800.24
810.44
820.0169
830.673
840.537
850.0289
860.181
870.94
880.711
890.152
90.285
900.338
910.714
920.0371
930.0769
940.0235
950.125
960.206
970.633
980.206
990.668



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: CNhs12005


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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