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FF:10040-101F4: 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 16:29, 29 March 2012


Name:frontal lobe, adult, pool1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuefrontal lobe
dev stage32-61 years old adult
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 number8121115A
catalog numberCat:636563
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-Neural0.39
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-penis0.118
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-0.304
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0.0518
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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: CNhs10647

Jaspar motifP-value
MA0002.20.0101
MA0003.10.347
MA0004.10.435
MA0006.10.336
MA0007.10.164
MA0009.10.147
MA0014.10.655
MA0017.10.0029
MA0018.20.0696
MA0019.10.942
MA0024.10.956
MA0025.10.269
MA0027.10.533
MA0028.10.152
MA0029.10.0608
MA0030.10.245
MA0031.10.981
MA0035.20.0752
MA0038.10.0617
MA0039.20.209
MA0040.10.585
MA0041.10.544
MA0042.10.705
MA0043.10.38
MA0046.10.0365
MA0047.20.0833
MA0048.10.12
MA0050.10.01
MA0051.10.139
MA0052.10.127
MA0055.10.00352
MA0057.10.91
MA0058.10.377
MA0059.10.0781
MA0060.10.312
MA0061.10.00927
MA0062.20.0374
MA0065.22.96488e-4
MA0066.10.0216
MA0067.10.699
MA0068.10.582
MA0069.10.369
MA0070.10.254
MA0071.10.023
MA0072.10.383
MA0073.10.325
MA0074.10.171
MA0076.10.371
MA0077.10.216
MA0078.10.744
MA0079.20.487
MA0080.21.767e-8
MA0081.10.0665
MA0083.10.0709
MA0084.10.713
MA0087.10.417
MA0088.10.165
MA0090.10.269
MA0091.10.434
MA0092.10.363
MA0093.10.459
MA0099.22.83501e-12
MA0100.10.717
MA0101.10.00484
MA0102.20.174
MA0103.10.198
MA0104.20.448
MA0105.17.91022e-4
MA0106.10.0304
MA0107.10.00796
MA0108.20.954
MA0111.10.46
MA0112.28.39059e-4
MA0113.10.238
MA0114.10.00286
MA0115.10.304
MA0116.10.00433
MA0117.10.976
MA0119.10.052
MA0122.10.785
MA0124.10.696
MA0125.10.217
MA0131.10.992
MA0135.10.0261
MA0136.12.71832e-10
MA0137.20.47
MA0138.20.227
MA0139.10.421
MA0140.10.00926
MA0141.10.00706
MA0142.10.994
MA0143.10.973
MA0144.10.26
MA0145.10.208
MA0146.10.00879
MA0147.10.32
MA0148.10.109
MA0149.10.018
MA0150.10.00128
MA0152.10.91
MA0153.10.242
MA0154.10.0388
MA0155.10.571
MA0156.11.94605e-5
MA0157.10.676
MA0159.10.0047
MA0160.10.025
MA0162.10.115
MA0163.17.82072e-6
MA0164.10.696
MA0258.10.00891
MA0259.10.803



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: CNhs10647

Novel motifP-value
10.0377
100.0335
1000.3
1010.674
1020.781
1030.219
1040.136
1050.299
1060.0439
1070.115
1080.806
1090.00725
110.0148
1100.0462
1110.0624
1120.292
1130.604
1140.0936
1150.89
1160.148
1170.0107
1180.116
1190.0942
120.684
1200.162
1210.587
1220.673
1230.679
1240.0379
1250.215
1260.0316
1270.465
1280.14
1290.547
130.00151
1300.475
1310.0647
1320.767
1330.00497
1340.303
1350.193
1360.00943
1370.785
1380.866
1390.0742
140.846
1400.0792
1410.273
1420.764
1430.0194
1440.891
1450.0842
1460.586
1470.936
1480.154
1490.284
150.0739
1500.173
1510.622
1520.114
1530.775
1540.571
1550.462
1560.428
1570.433
1580.605
1590.0412
160.0722
1600.185
1610.198
1620.985
1630.776
1640.0205
1650.0403
1660.847
1670.422
1680.672
1690.00743
170.147
180.19
190.182
20.947
200.104
210.07
220.219
230.388
240.1
250.48
261.14024e-4
270.916
280.691
290.0139
30.0314
300.686
310.885
320.0205
330.0735
340.706
350.498
360.115
370.0383
380.302
390.218
40.866
400.0483
410.385
420.206
430.102
440.0754
450.759
460.0592
470.0614
480.0546
490.135
50.501
500.342
510.508
520.579
530.929
540.452
550.39
560.459
570.239
580.31
590.116
60.592
600.0705
610.0726
620.164
630.15
640.201
650.241
660.295
670.331
680.361
690.269
70.0618
700.0238
710.0113
720.484
730.04
740.767
750.033
760.438
770.186
780.00297
790.143
80.0491
800.912
810.559
820.461
830.162
840.638
850.184
860.209
870.00343
880.848
890.514
90.479
900.0523
910.458
920.438
930.714
940.0765
950.025
960.941
970.768
980.193
990.673



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: CNhs10647


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)
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)
0001870 (frontal cortex)
0001890 (forebrain)
0001893 (telencephalon)
0001950 (neocortex)
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)
0007023 (adult organism)
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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