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FF:10073-102A1: 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 16:53, 29 March 2012


Name:occipital lobe, fetal, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueoccipital lobe
dev stage22 weeks fetus
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberA602123
catalog numberCat:RtHFN: Brain occiptal lobe
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-Neural1.014
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-penis0.00234
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
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: CNhs11784

Jaspar motifP-value
MA0002.27.59244e-4
MA0003.10.193
MA0004.10.419
MA0006.10.246
MA0007.10.134
MA0009.10.203
MA0014.10.562
MA0017.10.00385
MA0018.20.172
MA0019.10.214
MA0024.10.191
MA0025.10.0646
MA0027.10.413
MA0028.10.446
MA0029.10.0898
MA0030.10.555
MA0031.10.0663
MA0035.20.027
MA0038.10.146
MA0039.20.123
MA0040.10.815
MA0041.10.426
MA0042.10.599
MA0043.10.806
MA0046.10.063
MA0047.20.00224
MA0048.10.701
MA0050.15.18325e-5
MA0051.10.00872
MA0052.10.124
MA0055.10.114
MA0057.10.299
MA0058.10.291
MA0059.10.185
MA0060.10.146
MA0061.10.0171
MA0062.20.0929
MA0065.23.59073e-4
MA0066.10.0138
MA0067.10.99
MA0068.10.152
MA0069.10.46
MA0070.10.29
MA0071.10.0622
MA0072.10.344
MA0073.10.214
MA0074.10.177
MA0076.10.727
MA0077.10.2
MA0078.10.623
MA0079.20.966
MA0080.21.71288e-11
MA0081.10.0555
MA0083.10.00305
MA0084.10.668
MA0087.10.378
MA0088.10.241
MA0090.10.133
MA0091.10.302
MA0092.10.408
MA0093.10.423
MA0099.24.66246e-20
MA0100.10.927
MA0101.10.00826
MA0102.20.0349
MA0103.10.164
MA0104.20.725
MA0105.10.0076
MA0106.10.0555
MA0107.10.0105
MA0108.20.238
MA0111.10.634
MA0112.21.60056e-4
MA0113.10.0481
MA0114.10.00916
MA0115.10.345
MA0116.10.012
MA0117.10.824
MA0119.10.135
MA0122.10.353
MA0124.10.705
MA0125.10.391
MA0131.10.612
MA0135.10.418
MA0136.11.33364e-13
MA0137.20.153
MA0138.20.712
MA0139.10.238
MA0140.10.00134
MA0141.10.00561
MA0142.10.903
MA0143.10.534
MA0144.10.0917
MA0145.10.0909
MA0146.10.0133
MA0147.10.623
MA0148.10.0154
MA0149.10.0148
MA0150.14.90466e-5
MA0152.10.276
MA0153.10.246
MA0154.10.0245
MA0155.10.447
MA0156.13.31088e-7
MA0157.10.0449
MA0159.10.00234
MA0160.10.00968
MA0162.10.221
MA0163.12.66805e-4
MA0164.10.922
MA0258.10.0063
MA0259.10.973



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: CNhs11784

Novel motifP-value
10.0642
100.108
1000.537
1010.759
1020.865
1030.101
1040.105
1050.148
1060.0335
1070.0973
1080.971
1097.03297e-4
110.0283
1100.143
1110.377
1120.201
1130.417
1140.0557
1150.724
1160.349
1170.0293
1180.273
1190.216
120.504
1200.216
1210.399
1220.715
1230.137
1240.48
1250.51
1260.0142
1270.207
1280.147
1290.365
130.00461
1300.0777
1310.92
1320.711
1330.242
1340.928
1350.643
1360.0162
1370.475
1380.735
1390.0807
140.616
1400.647
1410.446
1420.676
1430.00768
1440.947
1450.339
1460.403
1470.956
1480.0402
1490.0771
150.0872
1500.287
1510.414
1520.0529
1530.84
1540.524
1550.799
1560.575
1570.461
1580.826
1590.269
160.0409
1600.247
1610.158
1620.588
1630.448
1640.0988
1650.192
1660.98
1670.788
1680.0509
1690.009
170.0777
180.216
190.124
20.564
200.536
210.158
220.092
230.178
240.0273
250.409
260.0193
270.425
280.636
290.0696
30.046
300.646
310.708
320.0383
330.136
340.545
350.555
360.182
370.0184
380.221
390.24
40.839
400.0419
410.279
420.202
430.113
440.245
450.565
460.178
470.0823
480.0795
490.175
50.317
500.322
510.365
520.359
530.982
540.297
550.64
560.372
570.585
580.215
590.0381
60.915
600.0524
610.0486
620.147
630.126
640.373
650.178
660.333
670.559
680.249
690.511
70.0524
700.0181
710.023
720.159
730.0198
740.533
750.0491
760.672
770.0929
780.0124
790.27
80.106
800.152
810.714
820.363
830.00566
840.906
850.0893
860.251
870.00143
880.696
890.206
90.262
900.384
910.89
920.211
930.985
940.135
950.00962
960.365
970.799
980.299
990.565



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: CNhs11784


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
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)
0000477 (anatomical cluster)
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)
0001950 (neocortex)
0002021 (occipital lobe)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002619 (regional part of cerebral cortex)
0002780 (regional part of forebrain)
0002791 (regional part of telencephalon)
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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