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FF:10085-102B4: 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 16:54, 29 March 2012


Name:brain, fetal, pool1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebrain
dev stage20-33 weeks fetus
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyClontech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number8101369A-5
catalog numberCat: 636643 Lot: 8101369A-5
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-Neural0.844
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-penis0.144
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-0.32
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
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: CNhs11797

Jaspar motifP-value
MA0002.20.00504
MA0003.10.253
MA0004.10.713
MA0006.10.328
MA0007.10.144
MA0009.10.123
MA0014.10.516
MA0017.10.00269
MA0018.20.0693
MA0019.10.575
MA0024.10.818
MA0025.10.303
MA0027.10.357
MA0028.10.0213
MA0029.10.131
MA0030.10.712
MA0031.10.462
MA0035.20.233
MA0038.10.0127
MA0039.20.17
MA0040.10.699
MA0041.10.787
MA0042.10.947
MA0043.10.841
MA0046.10.859
MA0047.20.0489
MA0048.10.264
MA0050.18.77636e-7
MA0051.10.00106
MA0052.10.0427
MA0055.10.0201
MA0057.10.505
MA0058.10.615
MA0059.10.244
MA0060.10.0326
MA0061.10.0248
MA0062.22.76307e-4
MA0065.20.00146
MA0066.10.0573
MA0067.10.818
MA0068.10.014
MA0069.10.21
MA0070.10.0364
MA0071.10.0965
MA0072.10.884
MA0073.10.315
MA0074.10.223
MA0076.10.0208
MA0077.10.193
MA0078.10.359
MA0079.20.736
MA0080.26.88182e-10
MA0081.10.0244
MA0083.10.0745
MA0084.10.775
MA0087.10.701
MA0088.10.101
MA0090.10.177
MA0091.10.848
MA0092.10.703
MA0093.10.733
MA0099.21.11733e-12
MA0100.10.717
MA0101.10.0105
MA0102.20.0174
MA0103.10.409
MA0104.20.837
MA0105.10.00655
MA0106.10.0467
MA0107.10.0225
MA0108.22.71463e-4
MA0111.10.495
MA0112.25.22808e-4
MA0113.10.178
MA0114.10.0053
MA0115.10.514
MA0116.10.0123
MA0117.10.986
MA0119.10.0956
MA0122.10.41
MA0124.10.855
MA0125.10.443
MA0131.10.801
MA0135.10.0571
MA0136.14.47534e-15
MA0137.20.0509
MA0138.20.084
MA0139.10.232
MA0140.10.0184
MA0141.10.0205
MA0142.10.429
MA0143.10.335
MA0144.10.0903
MA0145.10.144
MA0146.10.0122
MA0147.10.635
MA0148.10.0575
MA0149.10.0164
MA0150.13.51289e-5
MA0152.10.872
MA0153.10.714
MA0154.10.0439
MA0155.10.764
MA0156.15.64254e-10
MA0157.10.258
MA0159.10.00593
MA0160.10.0151
MA0162.10.181
MA0163.11.7709e-5
MA0164.10.776
MA0258.10.0162
MA0259.10.86



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: CNhs11797

Novel motifP-value
10.0385
100.0264
1000.327
1010.991
1020.631
1030.123
1040.174
1050.413
1060.0677
1070.134
1080.804
1098.23403e-4
110.0278
1100.113
1110.075
1120.356
1130.451
1140.047
1150.85
1160.218
1170.00655
1180.0861
1190.279
120.796
1200.235
1210.223
1220.68
1230.419
1240.25
1250.526
1260.00179
1270.573
1280.251
1290.72
137.62631e-4
1300.277
1310.727
1320.562
1330.0101
1340.606
1350.294
1360.00214
1370.607
1380.927
1390.137
140.818
1400.423
1410.342
1420.435
1430.0442
1440.746
1450.426
1460.758
1470.86
1480.127
1490.199
150.0492
1500.193
1510.52
1520.0878
1530.619
1540.508
1550.467
1560.865
1570.13
1580.636
1590.971
160.0223
1600.36
1610.0956
1620.291
1630.82
1640.0145
1650.0372
1660.942
1670.156
1680.277
1690.00656
170.21
180.452
190.147
20.78
200.216
210.103
220.154
230.358
240.0526
250.372
260.0102
270.747
280.456
290.00766
30.0171
300.735
310.933
320.0333
330.0964
340.991
350.659
360.228
370.0173
380.291
390.258
40.715
400.0877
410.524
420.163
430.147
440.109
450.86
460.202
470.0616
480.0452
490.266
50.21
500.364
510.494
520.495
530.772
540.331
550.205
560.439
570.395
580.181
590.0968
60.856
600.0624
610.0405
620.129
630.155
640.39
650.394
660.459
670.287
680.169
690.866
70.0322
700.00577
710.00653
720.218
730.024
740.495
750.0227
760.313
770.196
787.02851e-4
790.357
80.117
800.597
810.648
820.607
830.0836
840.692
850.273
860.199
870.0027
880.621
890.247
90.545
900.0579
910.641
920.541
930.283
940.269
950.00617
960.657
970.862
980.338
990.945



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: CNhs11797


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

UBERON: Anatomy
0000033 (head)
0000061 (anatomical structure)
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)
0001016 (nervous system)
0001017 (central nervous system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004121 (ectoderm-derived structure)
0005423 (developing anatomical structure)

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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