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FF:10082-102B1: 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 16:53, 29 March 2012


Name:colon, adult, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuecolon
dev stage23 years old adult
sexfemale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyClontech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number8101369A-2
catalog numberCat: 636643 Lot: 8101369A-2
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-penis0.478
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-0.0549
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: CNhs11794

Jaspar motifP-value
MA0002.20.243
MA0003.10.236
MA0004.10.151
MA0006.10.113
MA0007.10.24
MA0009.10.947
MA0014.10.852
MA0017.16.02771e-4
MA0018.20.104
MA0019.10.827
MA0024.10.829
MA0025.10.731
MA0027.10.75
MA0028.11.37605e-6
MA0029.10.874
MA0030.10.0302
MA0031.10.0346
MA0035.20.517
MA0038.10.867
MA0039.20.0922
MA0040.10.808
MA0041.10.675
MA0042.10.849
MA0043.10.00554
MA0046.17.634e-29
MA0047.20.00408
MA0048.10.133
MA0050.10.594
MA0051.10.819
MA0052.10.222
MA0055.10.0652
MA0057.10.344
MA0058.10.0178
MA0059.10.00153
MA0060.10.982
MA0061.12.59139e-4
MA0062.25.2035e-8
MA0065.20.421
MA0066.10.0535
MA0067.10.0585
MA0068.10.632
MA0069.10.21
MA0070.10.744
MA0071.10.968
MA0072.10.415
MA0073.10.797
MA0074.10.987
MA0076.11.08291e-7
MA0077.10.761
MA0078.10.0799
MA0079.20.167
MA0080.20.551
MA0081.10.0078
MA0083.11.76002e-5
MA0084.10.455
MA0087.10.591
MA0088.10.223
MA0090.10.404
MA0091.10.555
MA0092.10.723
MA0093.10.105
MA0099.25.91369e-14
MA0100.10.0937
MA0101.10.00137
MA0102.20.133
MA0103.14.39647e-4
MA0104.20.00313
MA0105.11.84141e-7
MA0106.10.0228
MA0107.10.00227
MA0108.24.61607e-13
MA0111.10.948
MA0112.20.933
MA0113.10.994
MA0114.10.00799
MA0115.10.0298
MA0116.10.00566
MA0117.10.0319
MA0119.10.82
MA0122.10.897
MA0124.10.891
MA0125.10.301
MA0131.10.143
MA0135.10.49
MA0136.10.0117
MA0137.20.159
MA0138.20.397
MA0139.10.201
MA0140.10.281
MA0141.10.303
MA0142.10.516
MA0143.10.0492
MA0144.10.461
MA0145.10.0968
MA0146.10.436
MA0147.10.00131
MA0148.10.0332
MA0149.10.424
MA0150.12.65358e-6
MA0152.10.957
MA0153.14.31298e-15
MA0154.10.342
MA0155.10.825
MA0156.14.074e-4
MA0157.10.94
MA0159.10.741
MA0160.10.591
MA0162.10.791
MA0163.17.48786e-5
MA0164.10.49
MA0258.10.729
MA0259.10.0264



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: CNhs11794

Novel motifP-value
10.28
100.0601
1000.296
1010.698
1020.43
1030.0183
1040.931
1050.0818
1060.621
1070.0347
1080.332
1090.618
110.539
1100.406
1110.157
1120.625
1130.439
1140.108
1150.879
1160.729
1170.0199
1180.298
1190.553
120.484
1200.148
1210.845
1220.962
1230.0395
1240.737
1250.257
1260.95
1270.111
1280.0195
1290.629
130.32
1300.844
1310.352
1320.00479
1330.0363
1340.0124
1350.121
1360.767
1370.104
1380.68
1390.37
140.499
1400.85
1410.282
1420.951
1430.0137
1440.763
1450.14
1460.269
1470.475
1480.91
1490.171
150.184
1500.605
1510.468
1520.186
1530.867
1540.937
1550.73
1560.556
1570.945
1580.379
1590.517
160.429
1600.903
1610.506
1620.0914
1630.927
1640.0701
1650.621
1660.476
1670.217
1680.169
1690.375
170.604
180.00666
190.375
20.0355
200.125
210.313
220.583
230.385
240.375
250.547
260.564
270.438
280.676
290.0511
30.7
300.048
310.711
320.749
330.0885
340.218
350.112
360.0362
370.262
380.416
390.337
40.967
400.627
410.104
420.357
430.76
440.756
450.17
460.461
470.432
480.527
490.777
50.735
500.434
510.805
520.101
530.164
540.711
550.361
560.639
570.263
580.81
590.841
60.654
600.358
610.819
620.848
630.833
640.971
650.286
660.138
670.0757
680.861
690.505
70.978
700.337
710.0781
720.389
730.923
740.426
750.00661
760.0166
770.0327
780.836
790.471
80.973
800.963
810.895
820.494
830.667
840.26
850.403
860.496
870.469
880.872
890.944
90.446
900.00414
910.0798
920.511
930.123
940.0431
950.15
960.444
970.936
980.972
990.0475



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: CNhs11794


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
0000059 (large intestine)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000160 (intestine)
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)
0001007 (digestive system)
0001062 (anatomical entity)
0001155 (colon)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004119 (endoderm-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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