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FF:10014-101C5: 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 16:26, 29 March 2012


Name:colon, 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
tissuecolon
dev stage62,83,84 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 -5
catalog numberCat:AM6000 Lot:0910061 -5
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-penis-0.0732
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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-Whole0.0368
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: CNhs10619

Jaspar motifP-value
MA0002.20.211
MA0003.10.113
MA0004.10.289
MA0006.10.0774
MA0007.10.0818
MA0009.10.778
MA0014.10.792
MA0017.17.05636e-16
MA0018.20.236
MA0019.10.0445
MA0024.10.13
MA0025.10.774
MA0027.10.95
MA0028.11.03542e-4
MA0029.10.742
MA0030.11.74849e-4
MA0031.10.00776
MA0035.20.00269
MA0038.10.994
MA0039.20.0618
MA0040.10.253
MA0041.10.185
MA0042.10.659
MA0043.10.0213
MA0046.14.00924e-52
MA0047.28.25214e-6
MA0048.10.01
MA0050.10.00639
MA0051.10.0166
MA0052.10.413
MA0055.10.00261
MA0057.10.503
MA0058.10.204
MA0059.10.00424
MA0060.10.481
MA0061.11.28102e-4
MA0062.21.00055e-5
MA0065.20.0356
MA0066.10.0658
MA0067.10.129
MA0068.10.0264
MA0069.10.344
MA0070.10.709
MA0071.10.35
MA0072.10.362
MA0073.10.845
MA0074.10.805
MA0076.16.81515e-5
MA0077.10.459
MA0078.10.0291
MA0079.20.0588
MA0080.20.676
MA0081.10.0521
MA0083.12.49012e-4
MA0084.10.289
MA0087.10.197
MA0088.10.158
MA0090.10.543
MA0091.10.644
MA0092.10.894
MA0093.10.273
MA0099.27.32179e-12
MA0100.10.133
MA0101.10.00188
MA0102.20.714
MA0103.10.00355
MA0104.27.62393e-4
MA0105.11.33718e-6
MA0106.10.0145
MA0107.10.00342
MA0108.22.35791e-16
MA0111.10.733
MA0112.20.855
MA0113.10.264
MA0114.18.21563e-12
MA0115.13.32557e-7
MA0116.10.00154
MA0117.10.158
MA0119.10.392
MA0122.10.417
MA0124.10.351
MA0125.10.233
MA0131.10.195
MA0135.10.052
MA0136.10.659
MA0137.20.158
MA0138.20.14
MA0139.10.34
MA0140.10.731
MA0141.10.371
MA0142.10.24
MA0143.10.0636
MA0144.10.275
MA0145.10.158
MA0146.10.942
MA0147.12.39733e-4
MA0148.12.10988e-5
MA0149.10.0592
MA0150.14.04805e-5
MA0152.10.705
MA0153.13.62922e-32
MA0154.10.381
MA0155.10.672
MA0156.10.229
MA0157.10.531
MA0159.10.918
MA0160.10.734
MA0162.10.834
MA0163.17.35412e-6
MA0164.10.128
MA0258.10.438
MA0259.10.0322



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: CNhs10619

Novel motifP-value
10.122
100.0431
1000.226
1010.696
1020.162
1030.266
1040.938
1050.369
1060.642
1070.219
1080.746
1090.461
110.301
1100.124
1110.0758
1120.532
1130.864
1140.0645
1150.983
1160.582
1170.0292
1180.296
1190.705
120.843
1200.092
1210.767
1220.824
1230.167
1240.635
1250.0309
1260.14
1270.316
1280.195
1290.215
130.256
1300.605
1310.408
1320.0867
1330.00536
1340.0172
1350.174
1360.866
1370.341
1380.503
1390.0724
140.738
1400.261
1410.318
1420.764
1430.0247
1440.701
1450.415
1460.262
1470.65
1480.969
1490.134
150.0557
1500.61
1510.867
1520.0843
1530.993
1540.538
1550.822
1560.904
1570.413
1580.248
1590.716
160.342
1600.655
1610.458
1620.481
1630.811
1640.0502
1650.652
1660.239
1670.0894
1680.0323
1690.669
170.808
180.00772
190.43
20.0349
200.0656
210.194
220.563
230.551
240.643
250.61
260.342
270.568
280.84
290.0155
30.329
300.0117
310.839
320.366
330.378
340.272
350.199
360.0229
370.375
380.735
390.172
40.305
400.409
410.0836
420.447
430.482
440.761
450.162
460.215
470.27
480.446
490.0792
50.809
500.221
510.983
520.0599
530.649
540.77
550.479
560.857
570.073
580.945
590.47
60.863
600.372
610.576
620.612
630.957
640.527
650.707
660.0625
670.109
680.878
690.684
70.879
700.0639
710.0748
720.968
730.79
740.503
750.0175
760.009
770.0864
780.969
790.139
80.552
800.0296
810.145
820.409
830.726
840.747
850.464
860.887
870.951
880.793
890.875
90.498
900.0287
910.681
920.792
930.0535
940.0186
950.254
960.681
970.899
980.235
990.127



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: CNhs10619


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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