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FF:10188-103D8: 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 17:25, 29 March 2012


Name:cerebral meninges, adult
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sex66
ageM
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationNA
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberR1234043-10
sample typeNA
extraction protocol (Details)NA
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-Neural0.274
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-penis0.122
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-0.355
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0.0861
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs12840

Jaspar motifP-value
MA0002.20.0025
MA0003.10.357
MA0004.10.383
MA0006.10.499
MA0007.10.316
MA0009.10.101
MA0014.10.569
MA0017.10.00693
MA0018.20.0194
MA0019.10.381
MA0024.10.855
MA0025.10.0731
MA0027.10.545
MA0028.10.0345
MA0029.10.0132
MA0030.10.345
MA0031.10.742
MA0035.20.0582
MA0038.10.168
MA0039.20.192
MA0040.10.482
MA0041.10.197
MA0042.10.603
MA0043.10.312
MA0046.10.146
MA0047.20.123
MA0048.10.0924
MA0050.10.00417
MA0051.10.154
MA0052.10.0384
MA0055.10.00291
MA0057.10.975
MA0058.10.286
MA0059.10.0511
MA0060.10.501
MA0061.10.0104
MA0062.20.00212
MA0065.27.57239e-4
MA0066.10.0487
MA0067.10.68
MA0068.10.017
MA0069.10.553
MA0070.10.699
MA0071.10.0467
MA0072.10.33
MA0073.10.635
MA0074.10.279
MA0076.10.0705
MA0077.10.718
MA0078.10.592
MA0079.20.392
MA0080.23.85384e-9
MA0081.10.0194
MA0083.10.586
MA0084.10.901
MA0087.10.384
MA0088.10.0531
MA0090.10.64
MA0091.10.78
MA0092.10.47
MA0093.10.398
MA0099.29.94199e-11
MA0100.10.612
MA0101.10.00762
MA0102.20.275
MA0103.10.295
MA0104.20.297
MA0105.16.73866e-4
MA0106.10.0327
MA0107.10.0142
MA0108.25.11312e-4
MA0111.10.319
MA0112.20.00102
MA0113.10.283
MA0114.10.00415
MA0115.10.223
MA0116.10.00418
MA0117.10.963
MA0119.10.0404
MA0122.10.874
MA0124.10.95
MA0125.10.243
MA0131.10.807
MA0135.17.6368e-4
MA0136.18.38526e-13
MA0137.20.883
MA0138.20.143
MA0139.10.382
MA0140.10.00989
MA0141.10.0173
MA0142.10.671
MA0143.10.896
MA0144.10.458
MA0145.10.246
MA0146.10.00608
MA0147.10.204
MA0148.10.101
MA0149.10.0192
MA0150.10.00156
MA0152.10.493
MA0153.10.706
MA0154.10.0409
MA0155.10.712
MA0156.12.23484e-7
MA0157.10.505
MA0159.10.00637
MA0160.10.0375
MA0162.10.138
MA0163.12.13771e-6
MA0164.10.639
MA0258.10.00687
MA0259.10.634



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: CNhs12840

Novel motifP-value
10.0317
100.0241
1000.288
1010.955
1020.901
1030.244
1040.175
1050.171
1060.119
1070.217
1080.871
1090.0144
110.0143
1100.038
1110.0331
1120.628
1130.85
1140.066
1150.71
1160.285
1170.00642
1180.0862
1190.114
120.705
1200.129
1210.41
1220.575
1230.0772
1240.19
1250.303
1260.0728
1270.311
1280.308
1290.488
130.00191
1300.611
1310.0476
1320.84
1334.30079e-4
1340.405
1350.435
1360.0549
1370.642
1380.712
1390.141
140.696
1400.433
1410.364
1420.97
1430.0298
1440.877
1450.0655
1460.454
1470.961
1480.117
1490.344
150.0726
1500.208
1510.552
1520.182
1530.808
1540.857
1550.242
1560.39
1570.555
1580.305
1590.809
160.105
1600.21
1610.178
1620.986
1630.896
1640.0166
1650.0735
1660.763
1670.227
1680.533
1690.0071
170.182
180.315
190.211
20.98
200.101
210.0404
220.24
230.505
240.103
250.514
266.89302e-5
270.977
280.633
290.0107
30.0193
300.39
310.891
320.08
330.0856
340.744
350.495
360.048
370.0413
380.286
390.371
40.613
400.0231
410.472
420.136
430.0969
440.239
450.877
460.0626
470.0332
480.0309
490.0869
50.316
500.349
510.494
520.775
530.676
540.376
550.354
560.416
570.176
580.338
590.195
60.599
600.127
610.0516
620.202
630.131
640.22
650.298
660.21
670.279
680.134
690.479
70.0596
700.0264
710.00867
720.535
730.0512
740.944
750.0228
760.323
770.328
780.00179
790.1
80.0838
800.923
810.621
820.546
830.383
840.766
850.31
860.231
870.031
880.849
890.686
90.657
900.047
910.337
920.459
930.788
940.0511
950.0329
960.689
970.866
980.272
990.677



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: CNhs12840


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)
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)

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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