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FF:10163-103B1: 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 17:15, 29 March 2012


Name:occipital cortex, 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
tissueoccipital cortex
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-Neural0.357
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-penis1.039
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-0.272
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C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
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: CNhs12320

Jaspar motifP-value
MA0002.20.0443
MA0003.10.207
MA0004.10.339
MA0006.10.273
MA0007.10.356
MA0009.10.189
MA0014.10.638
MA0017.13.50006e-4
MA0018.20.546
MA0019.10.465
MA0024.10.64
MA0025.10.429
MA0027.10.627
MA0028.10.0564
MA0029.10.0687
MA0030.10.555
MA0031.10.816
MA0035.20.00513
MA0038.10.53
MA0039.20.135
MA0040.10.859
MA0041.10.374
MA0042.10.795
MA0043.10.874
MA0046.19.13091e-4
MA0047.20.0947
MA0048.10.186
MA0050.10.107
MA0051.10.114
MA0052.10.445
MA0055.10.00249
MA0057.10.786
MA0058.10.271
MA0059.10.0694
MA0060.10.682
MA0061.10.00783
MA0062.20.00259
MA0065.21.68703e-4
MA0066.10.00605
MA0067.10.875
MA0068.10.72
MA0069.10.616
MA0070.10.739
MA0071.10.0232
MA0072.10.343
MA0073.10.455
MA0074.10.26
MA0076.10.0852
MA0077.10.164
MA0078.10.794
MA0079.20.753
MA0080.24.09915e-7
MA0081.10.0262
MA0083.10.00509
MA0084.10.633
MA0087.10.853
MA0088.10.187
MA0090.10.409
MA0091.10.425
MA0092.10.254
MA0093.10.343
MA0099.27.65687e-21
MA0100.10.487
MA0101.10.00384
MA0102.20.19
MA0103.10.144
MA0104.20.396
MA0105.10.0013
MA0106.10.0475
MA0107.10.00434
MA0108.20.136
MA0111.10.612
MA0112.28.78094e-4
MA0113.10.573
MA0114.10.00117
MA0115.10.318
MA0116.10.00619
MA0117.10.853
MA0119.10.149
MA0122.10.782
MA0124.10.938
MA0125.10.523
MA0131.10.992
MA0135.10.167
MA0136.17.91622e-12
MA0137.20.321
MA0138.20.381
MA0139.10.349
MA0140.10.00233
MA0141.10.00255
MA0142.10.945
MA0143.10.486
MA0144.10.704
MA0145.10.168
MA0146.10.0169
MA0147.10.283
MA0148.10.0797
MA0149.10.0229
MA0150.11.35454e-4
MA0152.10.447
MA0153.10.0732
MA0154.10.043
MA0155.10.489
MA0156.11.62556e-7
MA0157.10.739
MA0159.10.00375
MA0160.10.00947
MA0162.10.113
MA0163.11.51358e-5
MA0164.10.875
MA0258.10.0099
MA0259.10.785



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: CNhs12320

Novel motifP-value
10.0607
100.0619
1000.401
1010.586
1020.977
1030.0634
1040.149
1050.109
1060.0535
1070.115
1080.943
1090.00144
110.0142
1100.0484
1110.221
1120.325
1130.579
1140.19
1150.943
1160.133
1170.0118
1180.143
1190.287
120.433
1200.209
1210.247
1220.797
1230.306
1240.201
1250.29
1260.0267
1270.401
1280.197
1290.567
130.00167
1300.121
1310.0673
1320.555
1330.127
1340.591
1350.322
1360.00119
1370.931
1380.947
1390.15
140.793
1400.916
1410.464
1420.53
1430.0928
1440.922
1450.144
1460.506
1470.903
1480.241
1490.161
150.105
1500.157
1510.673
1520.0806
1530.7
1540.428
1550.855
1560.556
1570.42
1580.139
1590.015
160.0303
1600.232
1610.252
1620.621
1630.721
1640.0576
1650.0707
1660.865
1670.814
1680.42
1690.0112
170.11
180.0762
190.207
20.801
200.202
210.0494
220.184
230.458
240.0219
250.443
265.56588e-4
270.625
280.654
290.00622
30.0513
300.869
310.918
320.0156
330.0501
340.636
350.596
360.16
370.0351
380.386
390.29
40.823
400.0282
410.277
420.229
430.133
440.132
450.656
460.063
470.0652
480.0675
490.293
50.753
500.438
510.364
520.543
530.734
540.373
550.774
560.461
570.43
580.302
590.0606
60.836
600.0785
610.077
620.17
630.244
640.196
650.271
660.169
670.433
680.152
690.417
70.0606
700.0574
710.00979
720.296
730.0249
740.956
750.0395
760.529
770.127
780.0047
790.4
80.0565
800.373
810.603
820.513
830.0695
840.723
850.225
860.233
875.05946e-5
880.738
890.258
90.301
900.0831
910.841
920.532
930.867
940.193
950.00869
960.894
970.762
980.267
990.552



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: CNhs12320


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)
0000064 (organ part)
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)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0000956 (cerebral cortex)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001869 (cerebral hemisphere)
0001890 (forebrain)
0001893 (telencephalon)
0001950 (neocortex)
0002021 (occipital lobe)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002619 (regional part of cerebral cortex)
0002780 (regional part of forebrain)
0002791 (regional part of telencephalon)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
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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