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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000075,CL:0000133,CL:0000144,CL:0000220,CL:0000221,CL:0000255,CL:0000548,CL:0000710,CL:0002077,CL:0002321,CL:0002371,CL:0002379
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000075,CL:0000133,CL:0000144,CL:0000220,CL:0000221,CL:0000255,CL:0000548,CL:0000710,CL:0002077,CL:0002321,CL:0002371,CL:0002379
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0104398
|fonse_cell_line=FF:0104398
|fonse_cell_line_closure=FF:0104398
|fonse_cell_line_closure=FF:0104398

Revision as of 17:02, 29 March 2012


Name:meningioma cell line:HKBMM
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebrain
dev stageNA
sexfemale
age48
cell typemeningeal cell
cell lineHKBMM
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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
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
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-0.143
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs11945

Jaspar motifP-value
MA0002.20.129
MA0003.10.396
MA0004.10.675
MA0006.10.131
MA0007.10.483
MA0009.10.257
MA0014.10.783
MA0017.10.144
MA0018.27.74611e-4
MA0019.10.888
MA0024.15.2969e-4
MA0025.10.0076
MA0027.10.97
MA0028.10.661
MA0029.10.866
MA0030.10.948
MA0031.10.624
MA0035.20.191
MA0038.10.00873
MA0039.20.377
MA0040.10.936
MA0041.10.63
MA0042.10.841
MA0043.19.43057e-7
MA0046.10.886
MA0047.20.0452
MA0048.10.258
MA0050.11.46612e-12
MA0051.18.76964e-13
MA0052.10.00655
MA0055.10.185
MA0057.10.0558
MA0058.10.202
MA0059.10.228
MA0060.16.46416e-7
MA0061.10.243
MA0062.24.38149e-4
MA0065.20.0122
MA0066.10.644
MA0067.10.0172
MA0068.10.557
MA0069.10.772
MA0070.10.398
MA0071.10.939
MA0072.10.387
MA0073.10.569
MA0074.10.238
MA0076.10.0247
MA0077.10.468
MA0078.10.896
MA0079.20.424
MA0080.21.17932e-5
MA0081.10.0109
MA0083.10.521
MA0084.10.407
MA0087.10.282
MA0088.10.552
MA0090.10.431
MA0091.10.813
MA0092.10.637
MA0093.10.62
MA0099.21.88231e-4
MA0100.10.115
MA0101.10.632
MA0102.20.0265
MA0103.10.00655
MA0104.20.678
MA0105.10.0569
MA0106.10.00441
MA0107.10.3
MA0108.20.285
MA0111.10.928
MA0112.20.00212
MA0113.10.51
MA0114.10.0672
MA0115.10.679
MA0116.10.0474
MA0117.10.171
MA0119.10.0208
MA0122.10.682
MA0124.10.0201
MA0125.10.295
MA0131.10.137
MA0135.10.226
MA0136.12.43628e-7
MA0137.20.0203
MA0138.20.956
MA0139.10.224
MA0140.10.996
MA0141.10.166
MA0142.10.034
MA0143.10.277
MA0144.10.568
MA0145.10.708
MA0146.10.0138
MA0147.10.64
MA0148.10.0121
MA0149.10.0901
MA0150.10.222
MA0152.10.647
MA0153.10.0873
MA0154.10.285
MA0155.10.938
MA0156.10.00105
MA0157.10.174
MA0159.10.236
MA0160.10.441
MA0162.10.157
MA0163.10.0165
MA0164.10.31
MA0258.10.0771
MA0259.10.503



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: CNhs11945

Novel motifP-value
10.247
100.318
1000.614
1010.46
1020.346
1030.292
1040.884
1050.284
1060.00199
1071.58123e-4
1080.0238
1090.0517
110.153
1100.282
1110.15
1120.309
1130.438
1140.0872
1150.166
1160.636
1170.458
1180.106
1190.338
120.171
1200.0209
1210.92
1220.317
1230.398
1240.201
1250.221
1260.575
1270.48
1280.146
1290.861
130.282
1300.0867
1310.465
1320.171
1330.538
1340.126
1350.399
1360.177
1370.534
1380.234
1390.0214
140.573
1400.896
1410.955
1420.808
1430.173
1440.822
1450.147
1460.67
1470.907
1480.189
1490.218
150.192
1500.0794
1510.285
1520.00325
1530.73
1540.93
1550.469
1560.8
1570.539
1580.163
1590.277
160.158
1600.485
1610.356
1620.258
1630.807
1640.23
1650.922
1660.731
1670.335
1680.685
1690.0304
170.269
180.0864
190.0714
20.556
200.415
210.301
220.314
230.0785
240.875
250.225
260.698
270.309
280.857
290.0834
30.0936
300.855
310.579
320.476
330.965
340.993
350.507
360.821
370.0656
380.652
390.213
40.738
400.789
410.344
420.336
430.231
440.017
450.43
460.0804
470.378
480.22
490.458
50.796
500.58
510.397
520.941
530.621
540.323
550.343
560.178
570.511
580.843
590.0119
60.846
600.469
610.423
620.537
630.194
640.493
650.148
660.642
670.467
680.679
690.168
70.61
700.0122
710.106
720.82
730.0152
740.461
750.0666
760.864
770.0893
780.0669
790.257
80.0429
800.0779
810.608
820.521
830.773
840.853
850.0292
860.748
870.00883
880.602
890.127
90.892
900.264
910.986
920.14
930.532
940.609
950.341
960.78
970.826
980.735
990.00531



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: CNhs11945


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000066 (epithelial cell)
0000075 (columnar/cuboidal epithelial cell)
0000133 (neurectodermal cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000710 (neurecto-epithelial cell)
0002077 (ecto-epithelial cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002379 (meningothelial cell)

DOID: Disease
0050686 (organ system cancer)
14566 (disease of cellular proliferation)
162 (cancer)
3093 (nervous system cancer)
3565 (meningioma)
3620 (central nervous system cancer)
4 (disease)

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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