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FF:10002-101A5: 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 16:11, 29 March 2012


Name:SABiosciences XpressRef Human Universal Total RNA, pool1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueunclassifiable
dev stageUNDEFINED
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companySABiosciences
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberB208251
catalog numberCat:GA-004
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
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-penis0.0104
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.0426
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
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0.236
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0.0426
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: CNhs10610

Jaspar motifP-value
MA0002.20.0661
MA0003.10.0446
MA0004.10.49
MA0006.10.0559
MA0007.10.128
MA0009.10.263
MA0014.10.643
MA0017.11.75288e-21
MA0018.20.207
MA0019.10.299
MA0024.10.0243
MA0025.10.0205
MA0027.10.549
MA0028.11.61278e-5
MA0029.10.915
MA0030.17.56008e-10
MA0031.18.37094e-10
MA0035.20.00481
MA0038.10.172
MA0039.20.0313
MA0040.10.15
MA0041.10.496
MA0042.10.463
MA0043.10.39
MA0046.17.69722e-78
MA0047.26.57631e-13
MA0048.10.0543
MA0050.10.0727
MA0051.10.365
MA0052.10.866
MA0055.10.14
MA0057.10.681
MA0058.10.447
MA0059.10.145
MA0060.10.454
MA0061.19.92051e-4
MA0062.22.31936e-8
MA0065.24.65912e-6
MA0066.10.911
MA0067.10.0331
MA0068.13.12494e-4
MA0069.10.414
MA0070.10.23
MA0071.10.628
MA0072.10.276
MA0073.10.746
MA0074.10.773
MA0076.18.36124e-6
MA0077.10.238
MA0078.10.0506
MA0079.20.145
MA0080.20.651
MA0081.10.0955
MA0083.10.673
MA0084.10.615
MA0087.10.183
MA0088.10.136
MA0090.10.00534
MA0091.10.642
MA0092.10.59
MA0093.10.479
MA0099.24.02614e-14
MA0100.10.0872
MA0101.10.00331
MA0102.20.0358
MA0103.10.111
MA0104.20.00751
MA0105.11.87939e-4
MA0106.10.586
MA0107.10.00211
MA0108.24.85909e-17
MA0111.10.853
MA0112.20.0405
MA0113.10.0124
MA0114.13.27221e-24
MA0115.17.23648e-6
MA0116.10.564
MA0117.10.229
MA0119.10.463
MA0122.10.646
MA0124.10.267
MA0125.10.151
MA0131.10.345
MA0135.10.57
MA0136.10.122
MA0137.24.05941e-5
MA0138.20.631
MA0139.10.706
MA0140.10.296
MA0141.10.0082
MA0142.10.621
MA0143.10.648
MA0144.13.12984e-4
MA0145.10.0194
MA0146.10.453
MA0147.10.00196
MA0148.14.64784e-9
MA0149.10.025
MA0150.10.0128
MA0152.10.00547
MA0153.19.55727e-44
MA0154.10.518
MA0155.10.297
MA0156.10.0534
MA0157.16.78354e-4
MA0159.10.00882
MA0160.10.0451
MA0162.10.685
MA0163.10.0319
MA0164.10.2
MA0258.10.177
MA0259.10.0167



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: CNhs10610

Novel motifP-value
10.548
100.128
1000.874
1010.71
1020.0159
1030.635
1040.964
1050.605
1060.227
1070.042
1080.878
1090.572
110.798
1100.67
1110.0234
1120.341
1130.081
1140.447
1150.988
1160.622
1170.0937
1180.631
1190.409
120.52
1200.398
1210.674
1220.927
1230.39
1240.435
1250.0634
1260.239
1270.0185
1280.692
1290.899
130.567
1300.487
1310.0467
1320.304
1330.357
1340.27
1350.17
1360.632
1370.712
1380.58
1390.285
140.497
1400.738
1410.628
1420.959
1430.00244
1440.124
1450.47
1460.0308
1470.943
1480.796
1490.414
150.545
1500.864
1510.493
1520.114
1530.79
1540.211
1550.603
1560.605
1570.906
1580.4
1590.526
160.613
1600.667
1610.986
1620.972
1630.969
1640.27
1650.0169
1660.719
1670.0923
1680.353
1690.124
170.814
180.016
190.0256
20.0545
200.223
210.269
220.171
230.11
240.897
250.618
260.83
270.621
280.752
290.0831
30.857
300.0432
310.727
320.825
330.542
340.161
350.419
360.143
370.743
380.685
390.115
40.0559
400.919
410.0236
420.907
430.984
440.581
450.0548
460.493
470.592
480.814
490.912
50.953
500.275
510.803
520.0638
530.714
540.755
550.809
560.671
570.175
580.64
590.499
60.34
600.214
610.431
620.959
630.441
640.749
650.567
660.0925
670.128
680.186
690.428
70.415
700.243
710.601
720.403
730.577
740.418
750.0802
760.0106
770.00569
780.505
790.448
80.916
800.116
810.419
820.839
830.743
840.751
850.419
860.991
870.324
880.405
890.783
90.327
900.617
910.475
920.67
930.983
940.0652
950.188
960.849
970.218
980.35
990.142



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: CNhs10610


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

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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