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FF:10024-101D6: 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 16:27, 29 March 2012


Name:small intestine, adult, pool1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuesmall intestine
dev stage15,40,85 years old adult
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyAmbion
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number0910061 -15
catalog numberCat:AM6000 Lot:0910061 -15
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-ToTALLY-RNA-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
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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-Whole0.0323
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: CNhs10630

Jaspar motifP-value
MA0002.20.907
MA0003.10.0806
MA0004.10.0964
MA0006.10.0113
MA0007.10.0241
MA0009.10.44
MA0014.10.539
MA0017.11.22328e-36
MA0018.20.142
MA0019.10.0747
MA0024.10.0506
MA0025.10.823
MA0027.10.745
MA0028.10.00354
MA0029.10.157
MA0030.10.0427
MA0031.10.0563
MA0035.22.56289e-5
MA0038.10.275
MA0039.20.0249
MA0040.10.49
MA0041.10.738
MA0042.10.668
MA0043.10.0088
MA0046.17.14573e-65
MA0047.23.11653e-4
MA0048.10.0045
MA0050.14.79544e-7
MA0051.14.31987e-5
MA0052.10.426
MA0055.10.0157
MA0057.10.251
MA0058.10.0787
MA0059.10.0025
MA0060.10.0468
MA0061.13.75534e-4
MA0062.20.00518
MA0065.26.5988e-6
MA0066.10.418
MA0067.10.0924
MA0068.10.974
MA0069.10.588
MA0070.10.964
MA0071.10.445
MA0072.10.184
MA0073.10.916
MA0074.10.63
MA0076.10.00842
MA0077.10.223
MA0078.10.02
MA0079.20.0503
MA0080.20.0705
MA0081.10.135
MA0083.10.0456
MA0084.10.267
MA0087.10.135
MA0088.10.325
MA0090.10.76
MA0091.10.858
MA0092.10.937
MA0093.10.0983
MA0099.24.99044e-10
MA0100.10.151
MA0101.10.00317
MA0102.20.935
MA0103.18.60997e-6
MA0104.24.60337e-5
MA0105.15.86679e-5
MA0106.10.00724
MA0107.10.00394
MA0108.23.08244e-6
MA0111.10.929
MA0112.20.0664
MA0113.10.248
MA0114.12.39961e-35
MA0115.16.42133e-13
MA0116.10.0442
MA0117.10.15
MA0119.10.884
MA0122.10.745
MA0124.10.673
MA0125.10.439
MA0131.10.275
MA0135.10.0396
MA0136.10.228
MA0137.20.251
MA0138.20.295
MA0139.10.909
MA0140.10.886
MA0141.10.008
MA0142.10.578
MA0143.10.0759
MA0144.10.109
MA0145.10.0899
MA0146.10.428
MA0147.11.30709e-5
MA0148.12.88111e-5
MA0149.10.233
MA0150.13.28503e-4
MA0152.10.932
MA0153.18.14286e-42
MA0154.10.711
MA0155.10.84
MA0156.10.456
MA0157.10.811
MA0159.10.234
MA0160.10.135
MA0162.10.54
MA0163.10.00298
MA0164.10.0811
MA0258.10.465
MA0259.10.00565



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: CNhs10630

Novel motifP-value
10.451
100.163
1000.364
1010.77
1020.109
1030.575
1040.957
1050.127
1060.144
1070.0707
1080.642
1090.707
110.903
1100.259
1110.493
1120.0967
1130.662
1140.689
1150.769
1160.695
1170.0949
1180.734
1190.351
120.987
1200.249
1210.953
1220.589
1231
1240.993
1250.033
1260.0579
1270.805
1280.0342
1290.493
130.494
1300.845
1310.828
1320.0601
1330.0197
1340.06
1350.422
1360.706
1370.462
1380.568
1390.141
140.481
1400.838
1410.605
1420.792
1430.068
1440.504
1450.055
1460.215
1470.786
1480.616
1490.0444
150.431
1500.919
1510.575
1520.0473
1530.972
1540.667
1550.282
1560.852
1570.449
1580.649
1590.437
160.922
1600.731
1610.587
1620.603
1630.708
1640.357
1650.47
1660.496
1670.449
1680.00733
1690.247
170.474
180.00981
190.175
20.0109
200.171
210.535
220.425
230.287
240.768
250.773
260.794
270.421
280.805
290.0974
30.765
300.0207
310.869
320.495
330.744
340.352
350.565
360.0498
370.967
380.437
390.101
40.329
400.795
410.111
420.757
430.985
440.428
450.1
460.584
470.644
480.889
490.471
50.865
500.23
510.797
520.0298
530.347
540.569
550.928
560.671
570.201
580.595
590.362
60.882
600.106
610.832
620.998
630.662
640.924
650.394
660.0649
670.0775
680.543
690.981
70.772
700.587
710.436
720.712
730.363
740.284
750.102
760.0775
770.026
780.136
790.152
80.93
800.00717
810.252
820.967
830.79
840.821
850.18
860.97
870.569
880.461
890.754
90.475
900.101
910.725
920.205
930.293
940.0275
950.807
960.955
970.763
980.419
990.0858



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: CNhs10630


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)
0000160 (intestine)
0000383 (musculature of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001007 (digestive system)
0001015 (musculature)
0001062 (anatomical entity)
0001135 (smooth muscle tissue)
0001555 (digestive tract)
0002050 (embryonic structure)
0002108 (small intestine)
0002204 (musculoskeletal system)
0002385 (muscle tissue)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007023 (adult organism)
0007026 (primitive gut)

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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