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FF:10067-101I4: 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:rectum, 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
tissuerectum
dev stage19 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 numberA912096
catalog numberCat:RtHFN: Rectum
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-penis-0.0538
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-lymphoma0.203
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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: CNhs11777

Jaspar motifP-value
MA0002.28.56274e-5
MA0003.10.314
MA0004.10.202
MA0006.10.971
MA0007.10.425
MA0009.10.102
MA0014.10.354
MA0017.10.0604
MA0018.20.875
MA0019.10.501
MA0024.10.243
MA0025.10.334
MA0027.10.32
MA0028.10.00767
MA0029.10.918
MA0030.10.42
MA0031.10.857
MA0035.20.259
MA0038.10.174
MA0039.20.679
MA0040.10.744
MA0041.10.507
MA0042.10.798
MA0043.10.295
MA0046.11.9669e-6
MA0047.20.865
MA0048.10.577
MA0050.10.114
MA0051.10.086
MA0052.10.562
MA0055.10.0426
MA0057.10.724
MA0058.10.0936
MA0059.10.0142
MA0060.10.907
MA0061.10.00383
MA0062.25.46889e-5
MA0065.20.00119
MA0066.10.00692
MA0067.10.146
MA0068.10.00118
MA0069.10.516
MA0070.10.448
MA0071.10.0681
MA0072.10.0758
MA0073.10.366
MA0074.10.442
MA0076.10.00399
MA0077.10.586
MA0078.10.487
MA0079.20.65
MA0080.21.96989e-6
MA0081.10.0335
MA0083.10.0162
MA0084.10.554
MA0087.10.696
MA0088.10.198
MA0090.10.764
MA0091.10.853
MA0092.10.541
MA0093.10.212
MA0099.28.06385e-19
MA0100.10.725
MA0101.10.0092
MA0102.20.249
MA0103.10.352
MA0104.20.0297
MA0105.11.36636e-6
MA0106.10.0194
MA0107.10.00868
MA0108.29.63317e-6
MA0111.10.773
MA0112.26.5125e-5
MA0113.10.296
MA0114.10.0539
MA0115.10.102
MA0116.14.09546e-4
MA0117.10.374
MA0119.10.189
MA0122.10.506
MA0124.10.54
MA0125.10.323
MA0131.10.826
MA0135.10.318
MA0136.15.82489e-11
MA0137.20.857
MA0138.20.883
MA0139.10.0768
MA0140.10.069
MA0141.10.0122
MA0142.10.053
MA0143.10.489
MA0144.10.696
MA0145.10.356
MA0146.10.0903
MA0147.10.0229
MA0148.10.572
MA0149.10.0219
MA0150.12.0405e-7
MA0152.10.117
MA0153.12.64571e-5
MA0154.10.00262
MA0155.10.79
MA0156.11.21135e-5
MA0157.10.238
MA0159.10.0063
MA0160.10.00471
MA0162.10.443
MA0163.13.05532e-8
MA0164.10.455
MA0258.10.0103
MA0259.10.28



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: CNhs11777

Novel motifP-value
10.0199
100.0652
1000.337
1010.941
1020.545
1030.0595
1040.507
1050.828
1060.327
1070.877
1080.92
1090.00318
110.0539
1100.14
1110.0458
1120.127
1130.158
1140.00325
1150.89
1160.795
1170.00651
1180.132
1190.509
120.479
1200.134
1210.682
1220.442
1230.0489
1240.513
1250.581
1260.21
1270.0762
1280.954
1290.432
130.0497
1300.782
1310.753
1320.163
1330.338
1340.977
1350.901
1360.259
1370.198
1380.756
1390.16
140.564
1400.77
1410.0962
1420.852
1430.00641
1440.841
1450.984
1460.38
1470.7
1480.24
1490.346
150.0331
1500.418
1510.619
1520.313
1530.595
1540.603
1550.58
1560.111
1570.438
1580.61
1590.337
160.11
1600.425
1610.224
1620.324
1630.711
1640.0722
1650.583
1660.121
1670.0555
1680.158
1690.00808
170.364
180.0483
190.602
20.668
200.178
210.329
220.256
230.62
240.0356
250.303
260.0791
270.596
280.551
290.00622
30.0979
300.346
310.899
320.108
330.135
340.572
350.111
360.0207
370.0149
380.329
390.821
40.615
400.113
410.0218
420.203
430.105
440.419
450.947
460.0613
470.0359
480.123
490.161
50.237
500.987
510.535
520.676
530.657
540.685
550.06
560.56
570.343
580.339
590.0926
60.955
600.476
610.105
620.146
630.236
640.403
650.346
660.112
670.325
680.126
690.671
70.18
700.0192
710.0164
720.292
730.0503
740.44
750.00771
760.337
770.304
780.105
790.455
80.109
800.444
810.366
820.165
830.64
840.671
850.176
860.126
870.00366
880.703
890.13
90.73
900.0401
910.818
920.5
930.0359
940.068
950.0103
960.29
970.984
980.186
990.674



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: CNhs11777


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)
0000077 (mixed endoderm/mesoderm-derived structure)
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)
0000926 (mesoderm)
0001007 (digestive system)
0001046 (hindgut)
0001052 (rectum)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004907 (lower digestive tract)
0004921 (subdivision of digestive tract)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007026 (primitive gut)
0009142 (entire embryonic mesenchyme)

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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