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FF:10162-103A9: 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 17:14, 29 March 2012


Name:pituitary gland, adult, donor10252
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuepituitary gland
dev stageNA
sexfemale
age76
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationPeter Heutink
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-Neural0.0891
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-penis0.177
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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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: CNhs12229

Jaspar motifP-value
MA0002.20.00742
MA0003.10.229
MA0004.10.455
MA0006.10.414
MA0007.10.682
MA0009.10.824
MA0014.10.828
MA0017.10.0117
MA0018.20.00627
MA0019.10.948
MA0024.10.934
MA0025.10.0492
MA0027.10.0929
MA0028.10.546
MA0029.10.291
MA0030.10.0111
MA0031.10.35
MA0035.20.0476
MA0038.10.114
MA0039.20.875
MA0040.10.855
MA0041.10.978
MA0042.10.598
MA0043.19.78425e-4
MA0046.10.587
MA0047.20.501
MA0048.10.115
MA0050.10.602
MA0051.10.81
MA0052.10.436
MA0055.10.0639
MA0057.10.4
MA0058.10.437
MA0059.10.0388
MA0060.10.313
MA0061.10.00459
MA0062.20.617
MA0065.28.34784e-5
MA0066.10.0316
MA0067.10.656
MA0068.10.331
MA0069.10.821
MA0070.10.634
MA0071.10.0647
MA0072.10.81
MA0073.10.442
MA0074.10.0901
MA0076.10.0917
MA0077.10.88
MA0078.10.14
MA0079.20.59
MA0080.27.31671e-7
MA0081.10.258
MA0083.10.00285
MA0084.10.526
MA0087.10.171
MA0088.10.494
MA0090.10.459
MA0091.10.651
MA0092.10.126
MA0093.10.513
MA0099.22.15298e-11
MA0100.10.48
MA0101.10.0129
MA0102.20.182
MA0103.10.506
MA0104.20.353
MA0105.12.59279e-4
MA0106.10.0493
MA0107.10.0102
MA0108.20.624
MA0111.10.681
MA0112.21.34979e-4
MA0113.10.996
MA0114.10.00602
MA0115.10.555
MA0116.10.0023
MA0117.10.842
MA0119.10.0266
MA0122.10.303
MA0124.10.654
MA0125.10.0898
MA0131.10.641
MA0135.10.0588
MA0136.10.00126
MA0137.20.0213
MA0138.20.487
MA0139.10.309
MA0140.10.00387
MA0141.10.00941
MA0142.10.684
MA0143.10.27
MA0144.10.995
MA0145.10.191
MA0146.10.0543
MA0147.10.202
MA0148.10.261
MA0149.10.0125
MA0150.10.00985
MA0152.10.797
MA0153.10.871
MA0154.10.00716
MA0155.10.29
MA0156.10.0845
MA0157.10.957
MA0159.10.0399
MA0160.10.0387
MA0162.10.0777
MA0163.12.06095e-6
MA0164.10.558
MA0258.10.0041
MA0259.10.622



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: CNhs12229

Novel motifP-value
10.064
100.0594
1000.413
1010.685
1020.917
1030.102
1040.207
1050.807
1060.00122
1070.01
1080.393
1090.0148
110.0187
1100.0967
1110.0664
1120.487
1130.625
1140.0757
1150.642
1160.0675
1170.0675
1180.296
1190.0608
120.992
1200.138
1210.806
1220.605
1230.771
1240.704
1250.0583
1260.25
1270.322
1280.0305
1290.242
130.016
1300.34
1310.413
1320.888
1330.277
1340.559
1350.278
1360.174
1370.156
1380.735
1390.299
140.925
1400.694
1410.738
1420.294
1430.0322
1440.426
1450.0874
1460.451
1470.654
1480.0054
1490.125
150.116
1500.19
1510.508
1520.0575
1530.873
1540.891
1550.983
1560.77
1570.452
1580.0923
1590.0153
160.108
1600.0522
1610.337
1620.899
1630.753
1640.145
1650.245
1660.964
1670.911
1680.122
1690.00743
170.0467
180.0693
190.144
20.68
200.652
210.0816
220.148
230.0834
240.212
250.733
260.00383
270.459
280.793
290.0341
30.113
300.836
310.769
320.00886
330.156
340.496
350.395
360.0943
370.0639
380.194
390.188
40.758
400.065
410.192
420.381
430.102
440.0407
450.659
460.0424
470.0997
480.0951
490.147
50.372
500.332
510.285
520.194
530.94
540.33
550.651
560.558
570.203
580.507
590.0309
60.587
600.0301
610.166
620.176
630.0574
640.187
650.081
660.362
670.309
680.945
690.216
70.172
700.0365
710.0271
720.767
730.0621
740.282
750.0733
760.601
770.118
780.0212
790.374
80.0321
800.862
810.254
820.258
830.152
840.496
850.0474
860.305
870.00305
880.667
890.254
90.328
900.0906
910.523
920.447
930.792
940.114
950.0576
960.459
970.884
980.261
990.289



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: CNhs12229


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
0000007 (pituitary gland)
0000025 (tube)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000465 (material 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)
0000924 (ectoderm)
0000949 (endocrine system)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001890 (forebrain)
0001894 (diencephalon)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002368 (endocrine gland)
0002530 (gland)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0003296 (gland of diencephalon)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007023 (adult organism)
0007135 (neural keel)
0007284 (presumptive neural plate)

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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