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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100104
|fonse_cell_line=FF:0100104
|fonse_cell_line_closure=FF:0100104
|fonse_cell_line_closure=FF:0100104

Revision as of 16:32, 29 March 2012


Name:splenic lymphoma with villous lymphocytes cell line:SLVL
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stage70 year old adult
sexfemale
age70
cell typeb cell
cell lineSLVL
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-penis0.206
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-lymphoma0.516
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs10741

Jaspar motifP-value
MA0002.20.00755
MA0003.10.434
MA0004.10.023
MA0006.10.204
MA0007.10.319
MA0009.10.991
MA0014.10.946
MA0017.10.182
MA0018.20.164
MA0019.10.249
MA0024.15.72802e-5
MA0025.10.046
MA0027.10.889
MA0028.10.00197
MA0029.10.69
MA0030.10.412
MA0031.10.489
MA0035.20.956
MA0038.10.165
MA0039.20.566
MA0040.10.159
MA0041.10.156
MA0042.10.16
MA0043.10.11
MA0046.10.183
MA0047.20.966
MA0048.10.53
MA0050.15.56514e-14
MA0051.15.69981e-8
MA0052.10.547
MA0055.10.093
MA0057.10.518
MA0058.10.00795
MA0059.10.00248
MA0060.16.65793e-4
MA0061.14.38058e-9
MA0062.24.80053e-6
MA0065.20.0208
MA0066.10.609
MA0067.10.901
MA0068.10.0815
MA0069.10.471
MA0070.10.954
MA0071.10.32
MA0072.10.132
MA0073.10.775
MA0074.10.884
MA0076.11.90468e-4
MA0077.10.261
MA0078.10.2
MA0079.20.13
MA0080.21.10374e-4
MA0081.10.0416
MA0083.10.0715
MA0084.10.176
MA0087.10.469
MA0088.10.00363
MA0090.12.23316e-5
MA0091.10.888
MA0092.10.476
MA0093.10.0246
MA0099.20.135
MA0100.10.14
MA0101.19.64127e-9
MA0102.20.276
MA0103.10.107
MA0104.22.88772e-4
MA0105.11.03351e-9
MA0106.18.54524e-4
MA0107.11.09881e-8
MA0108.22.06408e-10
MA0111.10.42
MA0112.20.299
MA0113.10.551
MA0114.10.0534
MA0115.10.175
MA0116.14.8727e-5
MA0117.10.707
MA0119.10.542
MA0122.10.214
MA0124.10.496
MA0125.10.347
MA0131.10.321
MA0135.10.437
MA0136.19.41026e-5
MA0137.20.075
MA0138.20.313
MA0139.10.108
MA0140.10.468
MA0141.10.266
MA0142.10.455
MA0143.10.292
MA0144.10.0891
MA0145.10.533
MA0146.10.697
MA0147.12.05343e-4
MA0148.10.574
MA0149.10.178
MA0150.10.495
MA0152.10.526
MA0153.10.104
MA0154.10.00255
MA0155.10.631
MA0156.15.72192e-4
MA0157.10.96
MA0159.10.543
MA0160.10.0545
MA0162.10.912
MA0163.12.1868e-11
MA0164.10.466
MA0258.10.103
MA0259.10.0245



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: CNhs10741

Novel motifP-value
10.00799
100.0144
1000.495
1010.195
1020.624
1030.0876
1040.433
1050.675
1060.957
1070.717
1080.747
1090.0777
110.167
1100.114
1110.0149
1120.104
1130.671
1140.207
1150.623
1160.627
1170.0188
1180.128
1190.102
120.852
1200.55
1210.363
1220.371
1231.30856e-4
1240.0615
1250.67
1260.117
1270.509
1280.347
1290.39
130.0635
1300.995
1310.221
1320.572
1330.587
1340.612
1350.571
1360.281
1370.171
1380.857
1390.218
140.692
1400.193
1410.0628
1420.65
1430.304
1440.516
1450.179
1460.426
1470.0525
1480.115
1490.529
150.0523
1500.972
1510.924
1520.0633
1530.207
1540.905
1550.0875
1560.959
1570.247
1580.315
1590.337
160.785
1600.136
1610.00795
1620.975
1630.761
1640.208
1650.788
1660.265
1670.396
1680.844
1690.722
170.546
180.466
190.949
20.498
200.369
210.161
220.986
230.325
240.174
250.188
260.0839
270.742
280.696
290.0206
30.0885
300.0791
310.765
320.733
330.741
340.632
350.126
360.0175
370.329
380.335
390.547
40.665
400.387
410.653
420.114
430.282
440.167
450.409
460.19
470.0486
480.0903
490.16
50.644
500.952
510.671
520.428
530.35
540.767
550.957
560.75
570.081
580.136
590.662
60.886
600.814
610.0826
620.122
630.548
640.267
650.799
660.1
670.584
680.335
690.794
70.108
700.443
710.0238
720.264
730.96
740.551
750.00566
760.26
770.846
780.319
790.541
80.173
800.376
810.0625
820.867
830.64
840.215
850.877
860.24
870.319
880.794
890.668
90.639
900.0153
910.89
920.838
930.877
940.493
950.0446
960.24
970.271
980.374
990.23



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: CNhs10741


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

DOID: Disease
0050686 (organ system cancer)
0060058 (lymphoma)
0060083 (immune system cancer)
14566 (disease of cellular proliferation)
162 (cancer)
2531 (hematologic 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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