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FF:10070-101I7: 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, 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
tissuecolon
dev stage37 weeks fetus
sexfemale
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 numberB207218
catalog numberCat:RtHFN: Colon
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
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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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



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: CNhs11780

Jaspar motifP-value
MA0002.20.0127
MA0003.10.35
MA0004.10.0856
MA0006.10.221
MA0007.10.451
MA0009.10.879
MA0014.10.547
MA0017.11.5072e-5
MA0018.20.342
MA0019.10.844
MA0024.10.362
MA0025.10.484
MA0027.10.954
MA0028.16.85983e-8
MA0029.10.46
MA0030.10.00988
MA0031.10.0133
MA0035.20.581
MA0038.10.391
MA0039.20.252
MA0040.10.786
MA0041.10.468
MA0042.10.664
MA0043.10.0234
MA0046.11.78773e-41
MA0047.20.00948
MA0048.10.0701
MA0050.10.579
MA0051.10.657
MA0052.10.91
MA0055.13.95214e-4
MA0057.10.998
MA0058.10.0366
MA0059.10.00134
MA0060.10.0256
MA0061.13.59909e-4
MA0062.22.14524e-11
MA0065.20.849
MA0066.10.0572
MA0067.10.0808
MA0068.10.00229
MA0069.10.389
MA0070.10.313
MA0071.10.247
MA0072.10.0488
MA0073.10.443
MA0074.10.831
MA0076.11.8053e-9
MA0077.10.634
MA0078.10.161
MA0079.20.316
MA0080.20.16
MA0081.10.0234
MA0083.18.20716e-4
MA0084.10.633
MA0087.10.067
MA0088.10.0153
MA0090.10.765
MA0091.10.811
MA0092.10.787
MA0093.10.0708
MA0099.22.1391e-19
MA0100.10.0639
MA0101.18.72678e-4
MA0102.20.851
MA0103.10.0106
MA0104.29.87157e-5
MA0105.12.33739e-7
MA0106.10.00218
MA0107.10.0014
MA0108.22.93257e-13
MA0111.10.449
MA0112.20.0711
MA0113.10.67
MA0114.10.00149
MA0115.10.188
MA0116.10.00318
MA0117.10.138
MA0119.10.621
MA0122.10.772
MA0124.10.972
MA0125.10.496
MA0131.10.225
MA0135.10.388
MA0136.16.60742e-4
MA0137.20.987
MA0138.20.536
MA0139.10.158
MA0140.10.728
MA0141.10.505
MA0142.10.232
MA0143.10.505
MA0144.10.731
MA0145.10.478
MA0146.10.453
MA0147.12.76096e-5
MA0148.10.00803
MA0149.10.0316
MA0150.11.7347e-7
MA0152.10.534
MA0153.12.81148e-20
MA0154.10.0438
MA0155.10.705
MA0156.12.00953e-4
MA0157.10.561
MA0159.10.255
MA0160.10.184
MA0162.10.701
MA0163.13.12226e-6
MA0164.10.16
MA0258.10.201
MA0259.10.0926



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: CNhs11780

Novel motifP-value
10.0344
100.0573
1000.198
1010.897
1020.252
1030.156
1040.818
1050.318
1060.597
1070.0584
1080.217
1090.0318
110.24
1100.0642
1110.00993
1120.935
1130.0202
1140.00823
1150.396
1160.932
1170.0139
1180.558
1190.916
120.645
1200.392
1210.298
1220.756
1230.688
1240.962
1250.05
1260.749
1270.0791
1280.042
1290.94
130.0902
1300.932
1310.786
1320.0421
1330.264
1340.342
1350.563
1360.265
1370.291
1380.88
1390.16
140.924
1400.612
1410.126
1420.506
1430.0268
1440.906
1450.649
1460.178
1470.599
1480.581
1490.747
150.0467
1500.748
1510.864
1520.445
1530.723
1540.658
1550.708
1560.832
1570.944
1580.203
1590.93
160.337
1600.675
1610.363
1620.143
1630.55
1640.229
1650.923
1660.104
1670.0477
1680.534
1690.346
170.804
180.00235
190.539
20.0728
200.11
210.256
220.679
230.431
240.257
250.592
260.295
270.847
280.819
290.0146
30.443
300.0352
310.902
320.0135
330.112
340.26
350.115
360.0335
370.0665
380.835
390.341
40.436
400.237
410.208
420.232
430.366
440.943
450.425
460.156
470.167
480.303
490.229
50.626
500.374
510.916
520.0912
530.43
540.874
550.192
560.874
570.206
580.648
590.851
60.912
600.441
610.546
620.755
630.889
640.535
650.887
660.0161
670.12
680.765
690.954
70.399
700.133
710.0508
720.567
730.156
740.199
750.00283
760.192
770.485
780.646
790.667
80.246
800.832
810.765
820.43
830.246
840.723
850.264
860.178
870.0738
880.852
890.409
90.615
900.137
910.339
920.845
930.0657
940.0238
950.0109
960.836
970.552
980.121
990.132



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: CNhs11780


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)
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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