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FF:10165-103B3: 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:locus coeruleus, 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
tissuelocus coeruleus
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-Neural0.184
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-penis1.112
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-0.328
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0.0539
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0.455
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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: CNhs12322

Jaspar motifP-value
MA0002.20.0154
MA0003.10.213
MA0004.10.292
MA0006.10.373
MA0007.10.366
MA0009.10.073
MA0014.10.819
MA0017.10.0017
MA0018.20.161
MA0019.10.965
MA0024.10.71
MA0025.10.684
MA0027.10.526
MA0028.10.0843
MA0029.10.0755
MA0030.10.121
MA0031.10.259
MA0035.20.00814
MA0038.10.256
MA0039.20.275
MA0040.10.643
MA0041.10.553
MA0042.10.972
MA0043.10.979
MA0046.10.00274
MA0047.20.141
MA0048.10.146
MA0050.10.0393
MA0051.10.109
MA0052.10.404
MA0055.10.00339
MA0057.10.785
MA0058.10.357
MA0059.10.0795
MA0060.10.244
MA0061.10.0027
MA0062.20.00448
MA0065.26.38739e-4
MA0066.10.0119
MA0067.10.623
MA0068.10.893
MA0069.10.833
MA0070.10.28
MA0071.10.037
MA0072.10.427
MA0073.10.432
MA0074.10.209
MA0076.10.167
MA0077.10.0328
MA0078.10.992
MA0079.20.639
MA0080.23.68358e-7
MA0081.10.0371
MA0083.10.0164
MA0084.10.266
MA0087.10.329
MA0088.10.245
MA0090.10.195
MA0091.10.564
MA0092.10.315
MA0093.10.354
MA0099.21.323e-19
MA0100.10.648
MA0101.10.00136
MA0102.20.328
MA0103.10.0701
MA0104.20.375
MA0105.11.53698e-4
MA0106.10.0132
MA0107.19.84369e-4
MA0108.20.655
MA0111.10.577
MA0112.28.25204e-4
MA0113.10.637
MA0114.10.00346
MA0115.10.786
MA0116.10.00378
MA0117.10.875
MA0119.10.147
MA0122.10.888
MA0124.10.877
MA0125.10.256
MA0131.10.94
MA0135.10.0334
MA0136.11.35442e-10
MA0137.20.177
MA0138.20.236
MA0139.10.486
MA0140.10.00491
MA0141.10.00475
MA0142.10.358
MA0143.10.115
MA0144.10.744
MA0145.10.29
MA0146.10.027
MA0147.10.198
MA0148.10.121
MA0149.10.0179
MA0150.13.6487e-4
MA0152.10.578
MA0153.10.2
MA0154.10.0389
MA0155.10.643
MA0156.19.18479e-7
MA0157.10.924
MA0159.10.0106
MA0160.10.0264
MA0162.10.147
MA0163.12.69032e-7
MA0164.10.659
MA0258.10.0171
MA0259.10.713



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: CNhs12322

Novel motifP-value
10.0688
100.0453
1000.404
1010.621
1020.831
1030.0309
1040.0894
1050.103
1060.0188
1070.0774
1080.999
1090.00239
110.012
1100.0507
1110.16
1120.489
1130.537
1140.128
1150.985
1160.23
1170.0144
1180.217
1190.275
120.537
1200.191
1210.481
1220.977
1230.429
1240.205
1250.481
1260.034
1270.461
1280.129
1290.408
130.0024
1300.123
1310.0198
1320.499
1330.0363
1340.448
1350.145
1360.00363
1370.582
1380.933
1390.226
140.986
1400.51
1410.617
1420.88
1430.0185
1440.88
1450.284
1460.531
1470.714
1480.318
1490.105
150.0684
1500.122
1510.694
1520.0888
1530.833
1540.434
1550.884
1560.286
1570.366
1580.37
1590.0106
160.0397
1600.2
1610.213
1620.936
1630.632
1640.0172
1650.214
1660.877
1670.985
1680.494
1690.0137
170.091
180.0774
190.281
20.804
200.233
210.0583
220.256
230.356
240.0374
250.54
266.14321e-4
270.514
280.826
290.00751
30.0611
300.926
310.93
320.015
330.0584
340.687
350.531
360.246
370.05
380.367
390.293
40.827
400.0589
410.212
420.242
430.137
440.153
450.644
460.0398
470.072
480.0478
490.278
50.723
500.418
510.303
520.546
530.721
540.437
550.493
560.467
570.353
580.318
590.0609
60.677
600.0734
610.0893
620.141
630.201
640.15
650.244
660.123
670.391
680.184
690.339
70.0686
700.0349
710.00679
720.289
730.0464
740.873
750.0315
760.379
770.163
780.00108
790.289
80.061
800.267
810.494
820.665
830.0385
840.603
850.451
860.177
874.04906e-4
880.742
890.178
90.367
900.0917
910.701
920.459
930.663
940.139
950.0184
960.923
970.654
980.2
990.51



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: CNhs12322


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)
0000063 (organ segment)
0000064 (organ part)
0000073 (regional part of nervous system)
0000125 (neural nucleus)
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)
0000988 (pons)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001895 (metencephalon)
0002020 (gray matter)
0002028 (hindbrain)
0002050 (embryonic structure)
0002148 (locus ceruleus)
0002298 (brainstem)
0002308 (nucleus of brain)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002680 (regional part of metencephalon)
0003057 (chordal neural plate)
0003075 (neural plate)
0003076 (posterior neural tube)
0003528 (brain grey matter)
0004121 (ectoderm-derived structure)
0004732 (segmental subdivision of nervous system)
0004733 (segmental subdivision of hindbrain)
0005068 (neural rod)
0005423 (developing anatomical structure)
0006331 (brainstem nucleus)
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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