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FF:10179-103C8: 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:pineal 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
tissuepineal 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-penis0.447
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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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: CNhs13804

Jaspar motifP-value
MA0002.20.0245
MA0003.10.302
MA0004.10.354
MA0006.10.286
MA0007.10.227
MA0009.10.387
MA0014.10.45
MA0017.10.0135
MA0018.24.76074e-7
MA0019.10.618
MA0024.10.393
MA0025.10.23
MA0027.10.791
MA0028.10.196
MA0029.10.906
MA0030.10.581
MA0031.10.827
MA0035.20.323
MA0038.10.113
MA0039.20.162
MA0040.10.981
MA0041.10.423
MA0042.10.505
MA0043.10.253
MA0046.10.199
MA0047.20.0521
MA0048.10.0643
MA0050.10.00737
MA0051.10.0337
MA0052.10.0305
MA0055.10.0153
MA0057.10.664
MA0058.10.269
MA0059.10.023
MA0060.10.162
MA0061.10.00783
MA0062.20.0131
MA0065.20.00345
MA0066.10.145
MA0067.10.129
MA0068.10.576
MA0069.10.782
MA0070.10.635
MA0071.10.635
MA0072.10.156
MA0073.10.333
MA0074.10.559
MA0076.10.558
MA0077.10.73
MA0078.10.767
MA0079.20.882
MA0080.25.67053e-10
MA0081.10.0465
MA0083.10.139
MA0084.10.302
MA0087.10.824
MA0088.10.0933
MA0090.10.226
MA0091.10.526
MA0092.10.27
MA0093.10.401
MA0099.23.91547e-7
MA0100.10.958
MA0101.10.0043
MA0102.20.141
MA0103.10.287
MA0104.20.34
MA0105.10.00449
MA0106.10.0258
MA0107.10.00362
MA0108.20.536
MA0111.10.429
MA0112.20.00538
MA0113.10.124
MA0114.10.0121
MA0115.10.963
MA0116.10.00599
MA0117.10.824
MA0119.10.0589
MA0122.10.481
MA0124.10.815
MA0125.10.191
MA0131.10.924
MA0135.15.08768e-4
MA0136.11.55569e-10
MA0137.20.316
MA0138.20.37
MA0139.10.461
MA0140.10.312
MA0141.10.0851
MA0142.10.786
MA0143.10.643
MA0144.10.0508
MA0145.10.312
MA0146.10.0146
MA0147.10.201
MA0148.10.0189
MA0149.10.104
MA0150.10.0398
MA0152.10.686
MA0153.10.42
MA0154.10.0281
MA0155.10.591
MA0156.13.22759e-8
MA0157.10.189
MA0159.10.0592
MA0160.10.434
MA0162.10.0517
MA0163.14.97684e-5
MA0164.10.464
MA0258.10.0923
MA0259.10.525



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: CNhs13804

Novel motifP-value
10.0775
100.0327
1000.18
1010.926
1020.92
1030.0847
1040.213
1050.786
1060.0197
1070.0371
1080.924
1090.00657
110.024
1100.0426
1110.0194
1120.969
1130.565
1140.344
1150.696
1160.39
1170.00925
1180.0153
1190.175
120.981
1200.104
1210.346
1220.793
1230.217
1240.703
1250.544
1260.287
1270.949
1280.194
1290.347
130.00639
1300.266
1310.0417
1320.581
1330.0173
1340.794
1350.507
1360.0143
1370.948
1380.499
1390.618
140.985
1400.544
1410.569
1420.567
1430.29
1440.512
1450.0582
1460.154
1470.153
1480.0936
1490.204
150.0482
1500.18
1510.457
1520.0314
1530.665
1540.864
1550.633
1560.979
1570.441
1580.0269
1590.029
160.0939
1600.0303
1610.0742
1620.716
1630.794
1640.00648
1650.0329
1660.966
1670.356
1680.222
1690.0135
170.071
180.184
190.264
20.681
200.184
210.109
220.271
230.236
240.0383
250.459
261.22735e-4
270.83
280.801
290.00817
30.0406
300.677
310.918
320.0363
330.0625
340.742
350.955
360.126
370.0601
380.319
390.235
40.836
400.0304
410.251
420.294
430.121
440.114
450.765
460.0465
470.0638
480.0456
490.17
50.358
500.25
510.34
520.545
530.668
540.385
550.512
560.448
570.143
580.335
590.0747
60.553
600.112
610.0451
620.303
630.0487
640.301
650.168
660.179
670.356
680.332
690.192
70.166
700.00577
710.00428
720.518
730.0364
740.846
750.0285
760.227
770.157
780.0589
790.26
80.0137
800.871
810.24
820.867
830.229
840.335
850.305
860.466
873.04717e-4
880.959
890.367
90.793
900.0905
910.775
920.584
930.833
940.0553
950.0336
960.639
970.774
980.326
990.197



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: CNhs13804


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
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)
0001899 (epithalamus)
0001905 (pineal body)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002368 (endocrine gland)
0002530 (gland)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002757 (regional part of epithalamus)
0002780 (regional part of forebrain)
0002784 (regional part of diencephalon)
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)
0005408 (circumventricular organ)
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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