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|rna_box=101
|rna_box=101
|rna_catalog_number=Cat:RtHFN: Small Intestine: Duodenum
|rna_catalog_number=Cat:RtHFN: Small Intestine: Duodenum

Revision as of 17:39, 11 September 2012


Name:duodenum, fetal, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueduodenum
dev stage36 weeks fetus
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberA706076
catalog numberCat:RtHFN: Small Intestine: Duodenum
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
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C81-trachea-salivary-throat-aorta-eye-submaxillary-parotid0
C82-Basophils-CD14-Eosinophils-Natural-Peripheral-immature-CD340
C83-choriocarcinoma-pancreatic-placenta-chorionic-HES3GFP-testicular-amniotic0
C84-choriocarcinoma-pancreatic-Wilms-Mallassezderived-thymus-salivary-colon0
C85-neuroblastoma-carcinoid-retinoblastoma-small-pineal-rhabdomyosarcoma-medulloblastoma0
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
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



No results for this sample



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: CNhs11781

Jaspar motifP-value
MA0002.20.191
MA0003.10.338
MA0004.10.0588
MA0006.10.154
MA0007.11
MA0009.10.51
MA0014.10.576
MA0017.12.35264e-6
MA0018.20.233
MA0019.10.596
MA0024.10.143
MA0025.10.357
MA0027.10.605
MA0028.11.04388e-8
MA0029.10.926
MA0030.10.641
MA0031.10.984
MA0035.20.0672
MA0038.10.27
MA0039.20.708
MA0040.10.848
MA0041.10.504
MA0042.10.61
MA0043.10.0174
MA0046.19.67734e-36
MA0047.20.143
MA0048.10.117
MA0050.10.93
MA0051.10.525
MA0052.10.354
MA0055.10.0164
MA0057.10.693
MA0058.10.00408
MA0059.10.00774
MA0060.10.0068
MA0061.19.22595e-6
MA0062.21.62736e-11
MA0065.20.504
MA0066.10.847
MA0067.10.0601
MA0068.10.966
MA0069.10.876
MA0070.10.379
MA0071.10.339
MA0072.10.118
MA0073.10.312
MA0074.10.744
MA0076.11.21887e-9
MA0077.10.648
MA0078.10.808
MA0079.20.916
MA0080.20.0187
MA0081.10.00432
MA0083.10.0786
MA0084.10.55
MA0087.10.135
MA0088.10.196
MA0090.10.619
MA0091.10.812
MA0092.10.964
MA0093.10.0495
MA0099.25.25888e-21
MA0100.10.0663
MA0101.11.63389e-5
MA0102.20.0996
MA0103.16.51481e-4
MA0104.23.79441e-4
MA0105.11.22804e-7
MA0106.10.023
MA0107.16.15476e-5
MA0108.24.94024e-7
MA0111.10.247
MA0112.20.529
MA0113.10.775
MA0114.13.01239e-5
MA0115.10.329
MA0116.10.0207
MA0117.10.118
MA0119.10.672
MA0122.10.974
MA0124.10.427
MA0125.10.485
MA0131.10.87
MA0135.10.463
MA0136.15.60165e-6
MA0137.20.787
MA0138.20.0195
MA0139.10.154
MA0140.10.781
MA0141.10.35
MA0142.10.0795
MA0143.10.203
MA0144.10.461
MA0145.10.625
MA0146.10.725
MA0147.10.0012
MA0148.10.257
MA0149.10.0392
MA0150.16.44763e-8
MA0152.10.0583
MA0153.18.23369e-20
MA0154.10.17
MA0155.10.65
MA0156.15.00674e-6
MA0157.10.158
MA0159.10.535
MA0160.10.406
MA0162.10.898
MA0163.10.024
MA0164.10.326
MA0258.10.185
MA0259.10.048


library id: CNhs12997This sample isn't target for the analysis



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: CNhs11781

Novel motifP-value
10.38
100.229
1000.684
1010.185
1020.577
1030.124
1040.879
1050.884
1060.104
1070.033
1080.587
1090.0941
110.935
1100.538
1110.797
1120.352
1133.09125e-5
1140.256
1150.442
1160.22
1170.00534
1180.692
1190.0755
120.42
1200.554
1210.222
1220.1
1232.29302e-4
1240.95
1250.552
1260.322
1270.0975
1280.0136
1290.969
130.165
1300.522
1310.409
1320.00249
1330.0922
1340.768
1350.196
1360.244
1370.144
1380.94
1390.638
140.886
1400.266
1410.963
1420.772
1430.0158
1440.818
1450.0854
1460.418
1470.659
1480.759
1490.376
150.204
1500.654
1510.468
1520.585
1530.534
1540.267
1550.668
1560.452
1570.526
1580.881
1590.773
160.815
1600.74
1610.855
1620.25
1630.105
1640.73
1650.844
1660.288
1670.813
1680.649
1690.36
170.6
180.011
190.11
20.00642
200.0689
210.536
220.498
230.266
240.458
250.564
260.659
270.429
280.993
290.0273
30.936
300.0921
310.492
321.1628e-5
330.262
340.435
350.378
360.0934
370.0989
380.525
390.497
40.638
400.556
410.0203
420.664
430.92
440.908
450.652
460.618
470.497
480.851
490.596
50.451
500.563
510.672
520.077
530.0335
540.588
550.306
560.924
570.846
580.654
590.714
60.962
600.228
610.509
620.922
630.842
640.823
650.466
660.0198
670.264
680.381
690.953
70.921
700.684
710.415
720.375
730.0784
740.0674
750.00105
760.201
770.108
780.245
790.666
80.819
800.587
810.9
820.537
830.914
840.421
850.103
860.0394
870.00642
880.786
890.458
90.9
900.166
910.156
920.0701
930.394
940.0886
950.0368
960.721
970.953
980.428
990.0762


library id: CNhs12997

Novel motifP-value
10.0486
100.081
1000.436
1010.944
1020.911
1030.141
1040.115
1050.0772
1060.0276
1070.0926
1080.953
1095.8364e-4
110.0217
1100.13
1110.233
1120.28
1130.463
1140.0483
1150.55
1160.376
1170.0182
1180.238
1190.185
120.572
1200.248
1210.468
1220.794
1230.418
1240.229
1250.359
1260.0141
1270.209
1280.162
1290.433
130.00364
1300.0736
1310.762
1320.744
1330.268
1340.698
1350.83
1360.00654
1370.504
1380.791
1390.089
140.583
1400.431
1410.431
1420.972
1430.0166
1440.902
1450.219
1460.464
1470.962
1480.0348
1490.141
150.0928
1500.234
1510.445
1520.0362
1530.991
1540.542
1550.684
1560.336
1570.402
1580.787
1590.115
160.0475
1600.274
1610.24
1620.53
1630.495
1640.061
1650.23
1660.736
1670.599
1680.0753
1690.00899
170.0717
180.262
190.134
20.605
200.34
210.151
220.103
230.182
240.0457
250.477
260.0105
270.555
280.611
290.0523
30.0406
300.801
310.65
320.0584
330.147
340.533
350.648
360.128
370.0148
380.24
390.236
40.995
400.0298
410.219
420.178
430.109
440.198
450.6
460.222
470.0598
480.0615
490.144
50.266
500.333
510.415
520.35
530.821
540.326
550.729
560.436
570.463
580.211
590.0464
60.997
600.0421
610.04
620.159
630.14
640.416
650.212
660.353
670.468
680.257
690.536
70.0563
700.0292
710.02
720.177
730.0107
740.733
750.0401
760.468
770.102
780.00489
790.489
80.108
800.148
810.644
820.429
830.00226
840.941
850.0676
860.244
870.00102
880.749
890.255
90.315
900.199
910.912
920.282
930.824
940.128
950.00489
960.308
970.775
980.234
990.696



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: CNhs11781
library id: CNhs12997


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
0000468 (multi-cellular organism)
0000922 (embryo)
0000955 (brain)
0001871 (temporal lobe)
0000956 (cerebral cortex)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0003528 (brain grey matter)
0002791 (regional part of telencephalon)
0000467 (anatomical system)
0002619 (regional part of cerebral cortex)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)
0001950 (neocortex)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000999 (fetal tissue sample)
0000004 (tissue sample)
0010071 (human temporal lobe - fetal sample)

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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