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FF:10049-101G4: 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 16:51, 29 March 2012


Name:pancreas, 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
tissuepancreas
dev stage52 years old adult
sexmale
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 number8081302A
catalog numberCat:636577
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-penis0.278
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-0.487
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs11756

Jaspar motifP-value
MA0002.20.917
MA0003.10.316
MA0004.10.11
MA0006.10.248
MA0007.10.0612
MA0009.10.729
MA0014.10.912
MA0017.10.353
MA0018.20.231
MA0019.10.539
MA0024.18.93872e-5
MA0025.10.193
MA0027.10.588
MA0028.10.0244
MA0029.10.319
MA0030.10.108
MA0031.10.487
MA0035.20.00128
MA0038.10.0151
MA0039.20.736
MA0040.10.846
MA0041.10.478
MA0042.10.682
MA0043.10.224
MA0046.13.32612e-37
MA0047.20.117
MA0048.10.00292
MA0050.10.0117
MA0051.10.0559
MA0052.10.651
MA0055.10.109
MA0057.10.228
MA0058.10.457
MA0059.10.152
MA0060.10.00955
MA0061.11.45609e-4
MA0062.21.28654e-4
MA0065.20.0115
MA0066.10.53
MA0067.10.00899
MA0068.10.00598
MA0069.10.521
MA0070.10.266
MA0071.10.421
MA0072.10.181
MA0073.10.766
MA0074.10.853
MA0076.10.0175
MA0077.10.415
MA0078.10.159
MA0079.20.308
MA0080.23.85604e-4
MA0081.10.00147
MA0083.10.163
MA0084.10.168
MA0087.10.643
MA0088.10.22
MA0090.10.682
MA0091.10.0348
MA0092.10.412
MA0093.10.228
MA0099.26.35277e-13
MA0100.10.0126
MA0101.10.00262
MA0102.20.527
MA0103.11.30428e-9
MA0104.20.278
MA0105.11.75164e-5
MA0106.10.361
MA0107.17.18095e-4
MA0108.23.3911e-4
MA0111.10.991
MA0112.20.0462
MA0113.10.261
MA0114.10.0366
MA0115.10.115
MA0116.10.594
MA0117.10.418
MA0119.10.958
MA0122.10.604
MA0124.10.72
MA0125.10.729
MA0131.10.898
MA0135.10.89
MA0136.12.41151e-5
MA0137.20.721
MA0138.20.0249
MA0139.10.0451
MA0140.10.194
MA0141.10.00231
MA0142.10.89
MA0143.10.454
MA0144.10.711
MA0145.10.0548
MA0146.10.0703
MA0147.10.121
MA0148.10.223
MA0149.10.585
MA0150.11.85407e-4
MA0152.10.0741
MA0153.17.92616e-15
MA0154.10.793
MA0155.10.542
MA0156.11.06518e-4
MA0157.10.982
MA0159.10.069
MA0160.10.271
MA0162.10.857
MA0163.10.0663
MA0164.10.527
MA0258.10.249
MA0259.10.998



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: CNhs11756

Novel motifP-value
10.422
100.217
1000.367
1010.409
1020.886
1030.973
1040.318
1050.569
1060.104
1070.0483
1080.504
1090.356
110.445
1100.775
1110.828
1120.096
1130.527
1140.987
1150.391
1160.0248
1170.281
1180.411
1190.0146
120.636
1200.303
1210.381
1220.221
1232.14847e-4
1240.694
1250.539
1260.843
1270.753
1280.0707
1290.893
130.174
1300.233
1310.438
1320.0397
1330.379
1340.738
1350.71
1360.738
1370.0333
1380.818
1390.329
140.52
1400.817
1410.578
1420.572
1430.0256
1440.773
1450.149
1460.232
1470.693
1480.674
1490.302
150.736
1500.841
1510.0642
1520.0281
1530.138
1540.402
1550.325
1560.577
1570.637
1580.733
1590.211
160.798
1600.734
1610.907
1620.585
1630.268
1640.621
1650.942
1660.529
1670.811
1680.858
1690.0127
170.692
180.271
190.0214
20.0534
200.394
210.131
220.997
230.896
240.976
250.761
260.0772
270.629
280.979
290.332
30.655
300.423
310.377
320.592
330.85
340.797
350.576
360.487
370.828
380.212
390.501
40.79
400.587
410.0153
420.712
430.414
440.662
450.582
460.648
470.63
480.3
490.0875
50.9
500.816
510.933
520.238
530.607
540.363
550.916
560.602
570.722
580.558
590.203
60.746
600.288
610.821
620.776
630.411
640.46
650.213
660.0875
670.223
680.146
690.566
70.209
700.334
710.434
720.658
730.163
740.0211
750.445
760.768
770.015
780.154
790.715
80.134
800.261
810.894
820.636
830.498
840.424
850.0459
860.407
870.856
880.371
890.358
90.401
900.144
910.14
920.129
930.932
940.0533
950.826
960.506
970.637
980.563
990.456



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: CNhs11756


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)
0000077 (mixed endoderm/mesoderm-derived structure)
0000160 (intestine)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001007 (digestive system)
0001041 (foregut)
0001045 (midgut)
0001048 (primordium)
0001062 (anatomical entity)
0001264 (pancreas)
0001555 (digestive tract)
0002050 (embryonic structure)
0002075 (viscus)
0002100 (trunk)
0002108 (small intestine)
0002114 (duodenum)
0002323 (body cavity)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003104 (mesenchyme)
0003921 (pancreas primordium)
0003922 (pancreatic epithelial bud)
0003923 (dorsal pancreatic bud)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004458 (body cavity or lining)
0004921 (subdivision of digestive tract)
0005177 (trunk region element)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007023 (adult organism)
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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