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FF:10039-101F3: 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:insula, 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
tissueinsula
dev stage20-68 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 number3040372
catalog numberCat:636568
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-Neural0.412
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-penis0.0833
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-0.347
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0.0498
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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: CNhs10646

Jaspar motifP-value
MA0002.20.0104
MA0003.10.372
MA0004.10.479
MA0006.10.353
MA0007.10.157
MA0009.10.221
MA0014.10.651
MA0017.10.00288
MA0018.20.0643
MA0019.10.915
MA0024.10.916
MA0025.10.22
MA0027.10.408
MA0028.10.111
MA0029.10.0788
MA0030.10.236
MA0031.10.884
MA0035.20.124
MA0038.10.0375
MA0039.20.261
MA0040.10.54
MA0041.10.208
MA0042.10.643
MA0043.10.308
MA0046.10.0905
MA0047.20.0784
MA0048.10.112
MA0050.10.00805
MA0051.10.114
MA0052.10.0603
MA0055.10.00346
MA0057.10.925
MA0058.10.414
MA0059.10.077
MA0060.10.228
MA0061.10.00979
MA0062.20.0296
MA0065.24.07482e-4
MA0066.10.0239
MA0067.10.716
MA0068.10.326
MA0069.10.385
MA0070.10.0729
MA0071.10.0318
MA0072.10.507
MA0073.10.403
MA0074.10.172
MA0076.10.294
MA0077.10.294
MA0078.10.761
MA0079.20.386
MA0080.24.64257e-8
MA0081.10.0737
MA0083.10.146
MA0084.10.673
MA0087.10.407
MA0088.10.149
MA0090.10.237
MA0091.10.481
MA0092.10.374
MA0093.10.504
MA0099.22.38054e-10
MA0100.10.656
MA0101.10.00644
MA0102.20.245
MA0103.10.241
MA0104.20.46
MA0105.16.40256e-4
MA0106.10.0339
MA0107.10.01
MA0108.20.398
MA0111.10.431
MA0112.28.54365e-4
MA0113.10.236
MA0114.10.00294
MA0115.10.27
MA0116.10.0035
MA0117.10.955
MA0119.10.0458
MA0122.10.885
MA0124.10.696
MA0125.10.199
MA0131.10.953
MA0135.10.00505
MA0136.11.64938e-9
MA0137.20.303
MA0138.20.167
MA0139.10.385
MA0140.10.00705
MA0141.10.00871
MA0142.10.893
MA0143.10.992
MA0144.10.241
MA0145.10.227
MA0146.10.0114
MA0147.10.335
MA0148.10.0579
MA0149.10.0149
MA0150.10.00229
MA0152.10.893
MA0153.10.394
MA0154.10.037
MA0155.10.661
MA0156.14.3166e-5
MA0157.10.6
MA0159.10.00449
MA0160.10.0291
MA0162.10.104
MA0163.13.92487e-6
MA0164.10.747
MA0258.10.00949
MA0259.10.774



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: CNhs10646

Novel motifP-value
10.0313
100.0267
1000.268
1010.77
1020.746
1030.176
1040.15
1050.379
1060.0516
1070.119
1080.849
1090.00851
110.0142
1100.0453
1110.0648
1120.282
1130.691
1140.0734
1150.835
1160.175
1170.0095
1180.093
1190.0848
120.83
1200.135
1210.74
1220.535
1230.628
1240.0537
1250.15
1260.0307
1270.457
1280.16
1290.496
130.00151
1300.524
1310.0895
1320.734
1330.00281
1340.259
1350.231
1360.00884
1370.78
1380.895
1390.061
140.89
1400.171
1410.227
1420.892
1430.0126
1440.837
1450.087
1460.63
1470.833
1480.107
1490.3
150.0725
1500.168
1510.613
1520.126
1530.8
1540.591
1550.455
1560.387
1570.447
1580.848
1590.0801
160.0719
1600.192
1610.17
1620.947
1630.861
1640.0182
1650.0248
1660.884
1670.289
1680.582
1690.00726
170.155
180.2
190.191
20.972
200.0983
210.088
220.237
230.416
240.108
250.5
261.59508e-4
270.921
280.658
290.0111
30.0249
300.627
310.85
320.0298
330.0747
340.794
350.462
360.098
370.0353
380.307
390.24
40.978
400.0492
410.429
420.169
430.106
440.066
450.801
460.0581
470.0535
480.0479
490.125
50.43
500.355
510.513
520.625
530.905
540.461
550.396
560.47
570.237
580.303
590.133
60.547
600.0718
610.0591
620.175
630.148
640.2
650.277
660.301
670.327
680.303
690.368
70.0586
700.0151
710.0109
720.471
730.0432
740.607
750.0294
760.366
770.208
780.00309
790.176
80.0538
800.922
810.55
820.477
830.166
840.743
850.198
860.208
870.00614
880.851
890.54
90.54
900.0277
910.422
920.443
930.61
940.0685
950.0261
960.955
970.798
980.213
990.711



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: CNhs10646


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)
0001890 (forebrain)
0001893 (telencephalon)
0001950 (neocortex)
0002022 (insula)
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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