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FF:10180-103C9: 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 17:39, 29 March 2012


Name:pituitary gland - adult, donor10196
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
age60
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
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
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.402
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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: CNhs13805

Jaspar motifP-value
MA0002.20.00555
MA0003.10.215
MA0004.10.282
MA0006.10.293
MA0007.10.604
MA0009.10.672
MA0014.10.927
MA0017.10.0256
MA0018.22.49177e-4
MA0019.10.729
MA0024.10.292
MA0025.10.666
MA0027.10.193
MA0028.10.494
MA0029.10.223
MA0030.10.0561
MA0031.10.944
MA0035.20.0619
MA0038.10.867
MA0039.20.287
MA0040.10.918
MA0041.10.471
MA0042.10.425
MA0043.10.00744
MA0046.10.192
MA0047.20.192
MA0048.10.0365
MA0050.10.033
MA0051.10.232
MA0052.10.582
MA0055.10.0312
MA0057.10.362
MA0058.10.287
MA0059.10.0634
MA0060.10.456
MA0061.10.00122
MA0062.20.899
MA0065.21.68275e-4
MA0066.10.0862
MA0067.10.851
MA0068.10.0872
MA0069.10.77
MA0070.10.745
MA0071.10.0911
MA0072.10.462
MA0073.10.451
MA0074.10.0612
MA0076.10.0939
MA0077.10.823
MA0078.10.191
MA0079.20.545
MA0080.23.17484e-10
MA0081.10.105
MA0083.16.04598e-4
MA0084.10.498
MA0087.10.432
MA0088.10.542
MA0090.10.723
MA0091.10.694
MA0092.10.233
MA0093.10.301
MA0099.22.94101e-15
MA0100.10.563
MA0101.17.89905e-4
MA0102.20.579
MA0103.10.144
MA0104.20.305
MA0105.10.00216
MA0106.10.0344
MA0107.13.35378e-4
MA0108.20.497
MA0111.10.792
MA0112.25.51689e-4
MA0113.10.901
MA0114.10.00574
MA0115.10.801
MA0116.10.0108
MA0117.10.53
MA0119.10.0209
MA0122.10.281
MA0124.10.87
MA0125.10.326
MA0131.10.89
MA0135.10.0252
MA0136.12.57381e-6
MA0137.20.175
MA0138.20.0485
MA0139.10.473
MA0140.10.00346
MA0141.10.0271
MA0142.10.868
MA0143.10.437
MA0144.10.673
MA0145.10.0998
MA0146.10.00886
MA0147.10.219
MA0148.10.131
MA0149.10.0391
MA0150.10.00758
MA0152.10.739
MA0153.10.766
MA0154.10.0106
MA0155.10.455
MA0156.10.00258
MA0157.10.229
MA0159.10.258
MA0160.10.0482
MA0162.10.0605
MA0163.13.48736e-5
MA0164.10.487
MA0258.10.00552
MA0259.10.755



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: CNhs13805

Novel motifP-value
10.142
100.0569
1000.545
1010.765
1020.922
1030.123
1040.382
1050.419
1063.98295e-4
1070.0147
1080.733
1090.025
110.0428
1100.137
1110.188
1120.778
1130.361
1140.247
1150.964
1160.0836
1170.0806
1180.268
1190.129
120.982
1200.162
1210.735
1220.592
1230.466
1240.925
1250.26
1260.19
1270.357
1280.0444
1290.229
130.00818
1300.103
1310.167
1320.777
1330.0114
1340.558
1350.042
1360.167
1370.0181
1380.759
1390.683
140.996
1400.742
1410.955
1420.934
1430.0604
1440.564
1450.0913
1460.221
1470.802
1480.0446
1490.204
150.13
1500.132
1510.465
1520.0246
1530.852
1540.914
1550.755
1560.464
1570.326
1580.0501
1590.0149
160.163
1600.0353
1610.39
1620.836
1630.833
1640.189
1650.21
1660.752
1670.763
1680.0597
1690.00402
170.0648
180.11
190.139
20.517
200.747
210.0382
220.0493
230.0271
240.0678
250.699
260.0012
270.559
280.737
290.049
30.117
300.894
310.862
320.018
330.109
340.374
350.774
360.216
370.101
380.158
390.13
40.922
400.103
410.257
420.493
430.0913
440.262
450.455
460.0734
470.199
480.103
490.121
50.345
500.203
510.347
520.112
530.565
540.351
550.616
560.693
570.27
580.629
590.0184
60.409
600.0167
610.207
620.157
630.0394
640.272
650.0604
660.142
670.46
680.391
690.284
70.121
700.206
710.0426
720.956
730.0524
740.598
750.0997
760.769
770.0971
780.0228
790.71
80.0573
800.716
810.32
820.56
830.0457
840.366
850.165
860.218
875.59295e-4
880.41
890.579
90.239
900.344
910.639
920.761
930.534
940.284
950.11
960.496
970.842
980.601
990.281



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: CNhs13805


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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