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FF:11235-116D2: 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 16:35, 29 March 2012


Name:Astrocyte - cerebral cortex, donor1
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 number1086
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-0.0867
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-lymphoma0.606
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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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: CNhs10864

Jaspar motifP-value
MA0002.25.34034e-4
MA0003.10.0724
MA0004.10.135
MA0006.10.84
MA0007.10.283
MA0009.10.323
MA0014.10.692
MA0017.10.00203
MA0018.20.668
MA0019.10.717
MA0024.19.29176e-6
MA0025.10.189
MA0027.10.546
MA0028.10.354
MA0029.10.262
MA0030.10.288
MA0031.10.0468
MA0035.20.0295
MA0038.13.96053e-7
MA0039.20.524
MA0040.10.0563
MA0041.10.339
MA0042.10.367
MA0043.10.673
MA0046.10.468
MA0047.22.47978e-4
MA0048.10.53
MA0050.10.0449
MA0051.10.172
MA0052.10.029
MA0055.10.511
MA0057.10.26
MA0058.10.0936
MA0059.10.0625
MA0060.13.15009e-13
MA0061.10.00779
MA0062.20.671
MA0065.27.38446e-4
MA0066.10.0707
MA0067.10.493
MA0068.15.98816e-6
MA0069.10.866
MA0070.10.234
MA0071.10.107
MA0072.10.331
MA0073.10.776
MA0074.10.254
MA0076.10.161
MA0077.10.065
MA0078.10.663
MA0079.20.572
MA0080.27.46339e-14
MA0081.10.072
MA0083.10.882
MA0084.10.741
MA0087.10.819
MA0088.10.416
MA0090.10.4
MA0091.10.0133
MA0092.10.427
MA0093.10.159
MA0099.21.32257e-8
MA0100.10.271
MA0101.10.0448
MA0102.20.0216
MA0103.10.0236
MA0104.20.253
MA0105.13.25758e-4
MA0106.10.105
MA0107.10.0224
MA0108.20.375
MA0111.10.704
MA0112.28.13373e-5
MA0113.10.19
MA0114.10.0374
MA0115.10.614
MA0116.10.00202
MA0117.10.891
MA0119.10.287
MA0122.10.852
MA0124.10.106
MA0125.10.0036
MA0131.10.475
MA0135.10.675
MA0136.19.97685e-13
MA0137.20.652
MA0138.20.2
MA0139.10.278
MA0140.10.0278
MA0141.10.0256
MA0142.10.00439
MA0143.10.0158
MA0144.10.0961
MA0145.10.229
MA0146.10.0403
MA0147.10.218
MA0148.10.00575
MA0149.10.021
MA0150.13.29073e-4
MA0152.10.0605
MA0153.10.646
MA0154.10.00411
MA0155.10.623
MA0156.11.32052e-4
MA0157.10.0257
MA0159.10.0157
MA0160.10.0221
MA0162.10.4
MA0163.12.09135e-6
MA0164.10.443
MA0258.10.00377
MA0259.10.485



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: CNhs10864

Novel motifP-value
10.0532
100.108
1000.868
1010.982
1020.491
1030.0847
1040.526
1050.907
1060.0174
1070.683
1080.34
1090.0157
110.045
1100.204
1110.0138
1120.0245
1130.44
1140.00329
1150.447
1160.863
1170.0541
1180.229
1190.107
120.33
1200.193
1210.904
1220.412
1230.54
1240.463
1250.834
1260.162
1270.144
1280.293
1290.292
130.27
1300.115
1310.858
1320.98
1330.332
1340.668
1350.37
1360.418
1370.24
1380.0747
1390.00305
140.949
1400.0872
1410.235
1420.674
1436.41796e-4
1440.98
1450.916
1460.937
1470.534
1480.0622
1490.11
150.0999
1500.415
1510.324
1520.035
1530.488
1540.816
1550.0573
1560.566
1570.373
1580.195
1590.917
160.177
1600.164
1610.505
1620.903
1630.395
1640.0159
1650.296
1660.157
1670.77
1680.505
1690.00952
170.0799
180.0496
190.345
20.457
200.982
210.361
220.206
230.0647
240.545
250.518
260.18
270.182
280.943
290.0899
30.0823
300.954
310.697
320.023
330.486
340.624
350.291
360.193
370.0437
380.235
390.949
40.66
400.143
410.225
420.253
430.111
440.116
450.578
460.0637
470.132
480.197
490.12
50.198
500.631
510.277
520.486
530.803
540.296
550.238
560.43
570.485
580.181
590.0572
60.991
600.066
610.168
620.1
630.207
640.361
650.0893
660.503
670.418
680.551
690.557
70.311
700.0069
710.0593
720.176
730.0269
740.531
750.0411
760.25
770.107
780.134
790.0783
80.26
800.875
810.499
820.0432
830.94
840.338
850.00713
860.184
870.453
880.947
890.127
90.323
900.72
910.645
920.0363
930.0756
940.0643
950.0354
960.192
970.66
980.274
990.99



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: CNhs10864


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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