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FF:10151-102I7: 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:amygdala, 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
tissueamygdala
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-Neural0.406
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-penis0.857
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-0.308
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0.0572
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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: CNhs12311

Jaspar motifP-value
MA0002.20.0143
MA0003.10.226
MA0004.10.372
MA0006.10.279
MA0007.10.335
MA0009.10.0958
MA0014.10.658
MA0017.10.00116
MA0018.20.538
MA0019.10.589
MA0024.10.99
MA0025.10.826
MA0027.10.404
MA0028.10.0663
MA0029.10.0276
MA0030.10.631
MA0031.10.824
MA0035.20.00405
MA0038.10.385
MA0039.20.189
MA0040.10.677
MA0041.10.446
MA0042.10.919
MA0043.10.974
MA0046.10.00182
MA0047.20.0371
MA0048.10.188
MA0050.10.0613
MA0051.10.163
MA0052.10.906
MA0055.10.00313
MA0057.10.815
MA0058.10.295
MA0059.10.068
MA0060.10.698
MA0061.10.00825
MA0062.20.00351
MA0065.22.42865e-4
MA0066.10.00912
MA0067.10.934
MA0068.10.669
MA0069.10.396
MA0070.10.786
MA0071.10.0148
MA0072.10.261
MA0073.10.407
MA0074.10.211
MA0076.10.12
MA0077.10.198
MA0078.10.749
MA0079.20.612
MA0080.23.23671e-8
MA0081.10.04
MA0083.10.0183
MA0084.10.873
MA0087.10.744
MA0088.10.193
MA0090.10.371
MA0091.10.598
MA0092.10.274
MA0093.10.375
MA0099.23.22385e-18
MA0100.10.556
MA0101.10.0043
MA0102.20.203
MA0103.10.175
MA0104.20.434
MA0105.18.58906e-4
MA0106.10.0243
MA0107.10.00552
MA0108.20.327
MA0111.10.483
MA0112.26.33143e-4
MA0113.10.49
MA0114.10.00187
MA0115.10.316
MA0116.10.00696
MA0117.10.844
MA0119.10.114
MA0122.10.618
MA0124.10.672
MA0125.10.225
MA0131.10.992
MA0135.10.0506
MA0136.11.26195e-11
MA0137.20.656
MA0138.20.519
MA0139.10.368
MA0140.14.90543e-4
MA0141.10.00186
MA0142.10.994
MA0143.10.547
MA0144.10.301
MA0145.10.166
MA0146.10.0169
MA0147.10.301
MA0148.10.0357
MA0149.10.0193
MA0150.11.88282e-4
MA0152.10.51
MA0153.10.0796
MA0154.10.0401
MA0155.10.553
MA0156.11.04266e-7
MA0157.10.486
MA0159.10.00421
MA0160.10.00742
MA0162.10.102
MA0163.19.13749e-6
MA0164.10.708
MA0258.10.00847
MA0259.10.75



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: CNhs12311

Novel motifP-value
10.048
100.049
1000.374
1010.378
1020.9
1030.0703
1040.151
1050.207
1060.0436
1070.111
1080.993
1090.00174
110.013
1100.0577
1110.16
1120.275
1130.571
1140.106
1150.966
1160.205
1170.0122
1180.147
1190.164
120.633
1200.204
1210.194
1220.834
1230.747
1240.334
1250.242
1260.0335
1270.435
1280.187
1290.386
130.00218
1300.307
1310.0492
1320.648
1330.0678
1340.407
1350.325
1360.00345
1370.774
1380.908
1390.101
140.925
1400.837
1410.437
1420.794
1430.0375
1440.898
1450.172
1460.495
1470.94
1480.23
1490.201
150.0707
1500.16
1510.577
1520.0874
1530.99
1540.489
1550.582
1560.313
1570.459
1580.513
1590.0389
160.0496
1600.223
1610.159
1620.793
1630.796
1640.0425
1650.035
1660.81
1670.663
1680.398
1690.00987
170.125
180.112
190.201
20.8
200.202
210.0781
220.202
230.351
240.0392
250.49
267.77333e-4
270.673
280.684
290.00827
30.0482
300.936
310.806
320.0348
330.0517
340.654
350.58
360.131
370.0339
380.302
390.273
40.636
400.0252
410.263
420.215
430.119
440.155
450.651
460.078
470.0549
480.0462
490.201
50.483
500.371
510.384
520.511
530.803
540.386
550.566
560.468
570.374
580.283
590.0668
60.957
600.0653
610.0906
620.168
630.2
640.187
650.227
660.127
670.276
680.127
690.479
70.0527
700.0463
710.0101
720.347
730.0295
740.685
750.0315
760.42
770.166
780.00163
790.26
80.0762
800.383
810.638
820.588
830.0321
840.68
850.256
860.2
872.35461e-4
880.825
890.361
90.362
900.0733
910.698
920.583
930.883
940.192
950.0105
960.972
970.757
980.257
990.475



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: CNhs12311


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)
0000125 (neural nucleus)
0000153 (anterior region of body)
0000349 (limbic system)
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)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001869 (cerebral hemisphere)
0001876 (amygdala)
0001890 (forebrain)
0001893 (telencephalon)
0002020 (gray matter)
0002050 (embryonic structure)
0002308 (nucleus of brain)
0002346 (neurectoderm)
0002420 (basal ganglion)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002791 (regional part of telencephalon)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0003528 (brain grey matter)
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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