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FF:10064-101I1: 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 16:52, 29 March 2012


Name:small intestine, 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
tissuesmall intestine
dev stage16 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 numberB205082
catalog numberCat:RtHFN: Small intesti
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-penis0.277
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-lymphoma0.0851
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs11773

Jaspar motifP-value
MA0002.20.0172
MA0003.10.0993
MA0004.10.0801
MA0006.10.0547
MA0007.10.992
MA0009.10.634
MA0014.10.665
MA0017.11.13073e-20
MA0018.20.03
MA0019.10.322
MA0024.10.799
MA0025.10.125
MA0027.10.779
MA0028.10.00239
MA0029.10.854
MA0030.10.84
MA0031.10.622
MA0035.20.00178
MA0038.10.715
MA0039.20.445
MA0040.10.586
MA0041.10.454
MA0042.10.355
MA0043.16.72746e-5
MA0046.12.67096e-52
MA0047.20.214
MA0048.10.205
MA0050.10.0159
MA0051.10.081
MA0052.10.0652
MA0055.10.015
MA0057.10.363
MA0058.10.0667
MA0059.10.0103
MA0060.10.0641
MA0061.12.28612e-6
MA0062.21.70202e-5
MA0065.20.038
MA0066.10.477
MA0067.10.00592
MA0068.10.828
MA0069.10.659
MA0070.10.798
MA0071.10.316
MA0072.10.0448
MA0073.10.635
MA0074.10.669
MA0076.10.00505
MA0077.10.8
MA0078.10.116
MA0079.20.38
MA0080.20.0133
MA0081.10.0178
MA0083.10.697
MA0084.10.455
MA0087.10.0851
MA0088.10.0858
MA0090.10.899
MA0091.10.894
MA0092.10.497
MA0093.10.112
MA0099.22.74262e-24
MA0100.10.0612
MA0101.19.43511e-5
MA0102.20.0163
MA0103.10.00177
MA0104.21.91046e-5
MA0105.13.58552e-6
MA0106.17.69484e-4
MA0107.11.76213e-4
MA0108.24.38893e-5
MA0111.10.639
MA0112.20.382
MA0113.10.447
MA0114.16.68948e-18
MA0115.12.22327e-4
MA0116.10.079
MA0117.10.0356
MA0119.10.285
MA0122.10.915
MA0124.10.623
MA0125.10.67
MA0131.10.61
MA0135.10.479
MA0136.16.95427e-4
MA0137.20.269
MA0138.20.0958
MA0139.10.838
MA0140.10.777
MA0141.10.32
MA0142.10.264
MA0143.10.149
MA0144.10.134
MA0145.10.646
MA0146.10.624
MA0147.14.00149e-6
MA0148.10.142
MA0149.10.054
MA0150.15.96523e-12
MA0152.10.258
MA0153.19.70223e-33
MA0154.10.242
MA0155.10.553
MA0156.10.0111
MA0157.10.033
MA0159.10.464
MA0160.10.397
MA0162.10.248
MA0163.10.322
MA0164.10.271
MA0258.10.753
MA0259.10.0295



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: CNhs11773

Novel motifP-value
10.113
100.155
1000.601
1010.833
1020.226
1030.809
1040.597
1050.499
1060.391
1070.123
1080.647
1090.0999
110.54
1100.419
1110.391
1120.403
1130.0136
1140.15
1150.557
1160.427
1170.00723
1180.538
1190.646
120.796
1200.815
1210.319
1220.56
1230.854
1240.215
1250.346
1260.729
1270.277
1280.0416
1290.959
130.304
1300.83
1310.585
1320.0161
1330.52
1340.827
1350.436
1360.518
1370.108
1380.682
1390.0456
140.481
1400.668
1410.544
1420.908
1430.0103
1440.743
1450.622
1460.373
1470.547
1480.659
1490.208
150.136
1500.714
1510.805
1520.128
1530.839
1540.758
1550.743
1560.314
1570.773
1580.552
1590.205
160.763
1600.861
1610.907
1620.201
1630.204
1640.87
1650.855
1660.44
1670.371
1680.678
1690.7
170.902
180.00639
190.251
20.0172
200.0923
210.592
220.915
230.964
240.583
250.413
260.737
270.352
280.657
290.12
30.464
300.0527
310.665
320.00595
330.359
340.223
350.233
360.0161
370.115
380.867
390.336
40.482
400.834
410.0195
420.326
430.316
440.0478
450.475
460.384
470.454
480.95
490.0436
50.219
500.591
510.706
520.132
530.595
540.738
550.291
560.962
570.229
580.866
590.559
60.675
600.393
610.345
620.417
630.475
640.957
650.893
660.0101
670.432
680.279
690.706
70.552
700.248
710.071
720.451
730.478
740.0711
750.00534
760.162
770.132
780.45
790.238
80.456
800.807
810.291
820.742
830.724
840.99
850.747
860.148
870.0515
880.85
890.91
90.842
900.062
910.66
920.901
930.104
940.0368
950.19
960.411
970.152
980.409
990.0482



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: CNhs11773


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)
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)
0001555 (digestive tract)
0002050 (embryonic structure)
0002108 (small intestine)
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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