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FF:10041-101F5: 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:dura mater, adult, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuedura mater
dev stage59 years old adult
sexfemale
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 number3040808
catalog numberCat:636588
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-Neural0.0266
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-0.085
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.0266
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
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-Whole0.0266
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-Whole0.0266
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: CNhs10648

Jaspar motifP-value
MA0002.20.118
MA0003.10.864
MA0004.10.22
MA0006.10.747
MA0007.10.31
MA0009.10.202
MA0014.10.107
MA0017.10.193
MA0018.20.783
MA0019.10.347
MA0024.10.56
MA0025.10.18
MA0027.10.945
MA0028.14.16716e-4
MA0029.10.736
MA0030.10.102
MA0031.10.414
MA0035.20.14
MA0038.10.0807
MA0039.20.353
MA0040.10.695
MA0041.10.717
MA0042.10.489
MA0043.10.598
MA0046.10.863
MA0047.20.465
MA0048.10.195
MA0050.12.40134e-8
MA0051.10.00622
MA0052.17.88043e-4
MA0055.11.96231e-4
MA0057.10.858
MA0058.10.106
MA0059.10.00259
MA0060.10.419
MA0061.10.0517
MA0062.26.57212e-4
MA0065.20.00267
MA0066.10.00671
MA0067.10.396
MA0068.16.0929e-4
MA0069.10.864
MA0070.10.0988
MA0071.10.0472
MA0072.10.11
MA0073.10.666
MA0074.10.168
MA0076.10.00254
MA0077.10.567
MA0078.10.123
MA0079.20.337
MA0080.29.00629e-6
MA0081.10.381
MA0083.10.151
MA0084.10.99
MA0087.10.186
MA0088.10.00588
MA0090.10.664
MA0091.10.601
MA0092.10.801
MA0093.10.2
MA0099.22.78391e-9
MA0100.10.395
MA0101.10.292
MA0102.20.0184
MA0103.10.00691
MA0104.20.0105
MA0105.12.29009e-5
MA0106.10.00424
MA0107.10.505
MA0108.21.34009e-10
MA0111.10.529
MA0112.20.00688
MA0113.10.518
MA0114.10.0257
MA0115.10.0172
MA0116.10.00659
MA0117.10.609
MA0119.10.157
MA0122.10.795
MA0124.10.529
MA0125.10.467
MA0131.10.754
MA0135.10.0667
MA0136.10.0297
MA0137.23.66188e-4
MA0138.20.75
MA0139.10.0214
MA0140.10.364
MA0141.10.00542
MA0142.10.239
MA0143.10.876
MA0144.10.189
MA0145.10.994
MA0146.10.0666
MA0147.10.00452
MA0148.10.959
MA0149.10.0154
MA0150.10.007
MA0152.10.0336
MA0153.10.832
MA0154.10.0456
MA0155.10.853
MA0156.10.849
MA0157.10.719
MA0159.10.0306
MA0160.10.018
MA0162.10.181
MA0163.11.82324e-7
MA0164.10.292
MA0258.10.0176
MA0259.10.11



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: CNhs10648

Novel motifP-value
10.00557
100.0361
1000.0746
1010.461
1020.123
1030.0531
1040.844
1050.946
1060.829
1070.31
1080.443
1090.0165
110.051
1100.0806
1110.0226
1120.465
1130.0313
1140.0756
1150.589
1160.328
1170.00396
1180.0182
1190.271
120.72
1200.0245
1210.828
1220.674
1230.134
1240.398
1250.0763
1260.381
1270.645
1280.732
1290.0145
130.0299
1300.393
1310.279
1320.56
1332.27882e-4
1340.0842
1350.0413
1360.0939
1370.461
1380.993
1390.148
140.927
1400.0843
1410.238
1420.52
1430.0256
1440.77
1450.509
1460.821
1470.811
1480.26
1490.821
150.0335
1500.369
1510.581
1520.862
1530.963
1540.968
1550.344
1560.539
1570.858
1580.996
1590.402
160.0288
1600.174
1610.27
1620.965
1630.377
1640.012
1650.442
1660.505
1670.0127
1680.681
1690.0749
170.592
180.0831
190.926
20.496
200.0989
210.314
220.704
230.708
240.353
250.344
260.00853
270.99
280.59
290.00509
30.179
300.205
310.729
320.195
330.181
340.322
350.207
360.0561
370.0496
380.497
390.868
40.33
400.0741
410.209
420.353
430.167
440.104
450.614
460.101
470.0291
480.132
490.0853
50.393
500.655
510.618
520.324
530.723
540.7
550.837
560.57
570.0354
580.425
590.539
60.831
600.995
610.349
620.306
630.311
640.117
650.603
660.184
670.254
680.834
690.406
70.308
700.00665
710.0157
720.962
730.175
740.783
750.00693
760.112
770.86
780.0145
790.0986
80.138
800.0653
810.753
820.197
830.851
840.955
850.9
860.403
870.0123
880.761
890.304
90.446
900.0455
910.612
920.951
930.194
940.0643
950.0339
960.832
970.707
980.217
990.71



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: CNhs10648


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
0000061 (anatomical structure)
0000062 (organ)
0000073 (regional part of nervous system)
0000094 (membrane organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000926 (mesoderm)
0001016 (nervous system)
0001017 (central nervous system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002342 (neural crest)
0002346 (neurectoderm)
0002360 (meninx)
0002363 (dura mater)
0002532 (epiblast (generic))
0003075 (neural plate)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007023 (adult organism)
0007284 (presumptive neural plate)
0007645 (future meninx)
0007647 (ectomeninx)

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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