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FF:10063-101H9: 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 16:52, 29 March 2012


Name:temporal lobe, fetal, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuetemporal lobe
dev stage22 weeks fetus
sexfemale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberA702181
catalog numberCat:RtHFN: Brain temporal lobe
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-Neural0.968
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
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



No results for this sample



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: CNhs11772

Jaspar motifP-value
MA0002.28.35727e-4
MA0003.10.174
MA0004.10.458
MA0006.10.263
MA0007.10.157
MA0009.10.105
MA0014.10.581
MA0017.10.00353
MA0018.20.142
MA0019.10.261
MA0024.10.19
MA0025.10.103
MA0027.10.383
MA0028.10.345
MA0029.10.153
MA0030.10.572
MA0031.10.0842
MA0035.20.0457
MA0038.10.15
MA0039.20.127
MA0040.10.615
MA0041.10.476
MA0042.10.614
MA0043.10.781
MA0046.10.0675
MA0047.20.00659
MA0048.10.638
MA0050.12.80604e-5
MA0051.10.00454
MA0052.10.342
MA0055.10.072
MA0057.10.298
MA0058.10.32
MA0059.10.196
MA0060.10.0813
MA0061.10.0153
MA0062.20.0421
MA0065.22.81935e-4
MA0066.10.0148
MA0067.10.877
MA0068.10.167
MA0069.10.338
MA0070.10.396
MA0071.10.0604
MA0072.10.292
MA0073.10.181
MA0074.10.14
MA0076.10.587
MA0077.10.144
MA0078.10.654
MA0079.20.951
MA0080.28.1854e-11
MA0081.10.0532
MA0083.10.00781
MA0084.10.978
MA0087.10.598
MA0088.10.155
MA0090.10.289
MA0091.10.388
MA0092.10.375
MA0093.10.457
MA0099.23.36291e-20
MA0100.10.955
MA0101.10.0058
MA0102.20.0238
MA0103.10.235
MA0104.20.708
MA0105.10.00846
MA0106.10.044
MA0107.10.00713
MA0108.20.574
MA0111.10.625
MA0112.21.77974e-4
MA0113.10.0369
MA0114.10.00528
MA0115.10.318
MA0116.10.0141
MA0117.10.817
MA0119.10.154
MA0122.10.2
MA0124.10.706
MA0125.10.312
MA0131.10.603
MA0135.10.812
MA0136.17.10682e-14
MA0137.20.179
MA0138.20.555
MA0139.10.229
MA0140.10.00253
MA0141.10.00464
MA0142.10.598
MA0143.10.485
MA0144.10.0912
MA0145.10.105
MA0146.10.0162
MA0147.10.605
MA0148.10.0445
MA0149.10.00999
MA0150.13.22729e-5
MA0152.10.366
MA0153.10.184
MA0154.10.0252
MA0155.10.532
MA0156.11.21398e-7
MA0157.10.0493
MA0159.10.00178
MA0160.10.00676
MA0162.10.204
MA0163.11.24466e-4
MA0164.10.881
MA0258.10.00616
MA0259.10.985


library id: CNhs12996This sample isn't target for the analysis



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: CNhs11772

Novel motifP-value
10.0726
100.0945
1000.53
1010.819
1020.869
1030.0508
1040.105
1050.188
1060.0383
1070.129
1080.999
1094.6965e-4
110.025
1100.163
1110.318
1120.254
1130.283
1140.0553
1150.765
1160.403
1170.0261
1180.254
1190.267
120.563
1200.296
1210.324
1220.577
1230.0924
1240.347
1250.381
1260.0222
1270.216
1280.17
1290.403
130.0054
1300.0672
1310.644
1320.727
1330.356
1340.814
1350.719
1360.00994
1370.423
1380.676
1390.105
140.66
1400.73
1410.425
1420.842
1430.00585
1440.754
1450.305
1460.48
1470.956
1480.0435
1490.105
150.0668
1500.247
1510.437
1520.0454
1530.817
1540.466
1550.636
1560.527
1570.383
1580.816
1590.293
160.0367
1600.247
1610.15
1620.583
1630.393
1640.0925
1650.207
1660.995
1670.635
1680.0478
1690.0109
170.0817
180.216
190.131
20.567
200.538
210.202
220.0937
230.155
240.0309
250.387
260.0276
270.38
280.696
290.0544
30.0489
300.677
310.715
320.052
330.116
340.488
350.545
360.164
370.0149
380.267
390.26
40.988
400.0403
410.246
420.213
430.116
440.198
450.533
460.221
470.0701
480.0838
490.197
50.274
500.322
510.388
520.344
530.948
540.308
550.749
560.386
570.574
580.259
590.0359
60.973
600.0416
610.0463
620.157
630.145
640.44
650.217
660.289
670.548
680.164
690.447
70.0435
700.0233
710.0185
720.146
730.0151
740.901
750.0413
760.584
770.124
780.00884
790.293
80.105
800.139
810.668
820.348
830.00247
840.838
850.0824
860.216
878.98971e-4
880.704
890.182
90.246
900.505
910.853
920.266
930.514
940.142
950.00576
960.385
970.796
980.263
990.563


library id: CNhs12996

Novel motifP-value
10.25
100.181
1000.556
1010.769
1020.359
1030.7
1040.624
1050.119
1060.521
1070.0738
1080.333
1090.0774
110.576
1100.298
1110.43
1120.0648
1130.0118
1140.837
1150.111
1160.368
1170.00875
1180.668
1190.266
120.365
1200.64
1210.277
1220.173
1230.285
1240.476
1250.744
1260.628
1270.205
1280.136
1290.501
130.106
1300.162
1310.758
1320.0133
1330.49
1340.974
1350.0981
1360.499
1370.262
1380.853
1390.858
140.543
1400.921
1410.987
1420.727
1430.16
1440.773
1450.499
1460.647
1470.297
1480.0911
1490.153
150.191
1500.429
1510.489
1520.636
1530.847
1540.656
1550.539
1560.67
1570.574
1580.836
1590.126
160.791
1600.62
1610.688
1620.635
1630.388
1640.561
1650.517
1660.264
1670.579
1680.568
1690.801
170.957
180.0296
190.0251
20.00333
200.0105
210.469
220.716
230.197
240.539
250.592
260.726
270.087
280.573
290.0383
30.389
300.0791
310.489
323.21252e-6
330.362
340.535
350.999
360.0222
370.0818
380.715
390.689
40.477
400.0971
410.0118
420.259
430.914
440.313
450.684
460.902
470.563
480.633
490.615
50.736
500.982
510.644
520.235
530.854
540.762
550.822
560.784
570.234
580.85
590.158
60.872
600.384
610.246
620.909
630.711
640.915
650.654
660.00314
670.134
680.471
690.801
70.938
700.495
710.42
720.78
730.0187
740.21
750.0129
760.0166
770.252
780.582
790.166
80.862
800.284
810.501
820.501
830.979
840.742
850.109
860.177
870.00787
880.747
890.491
90.808
900.0592
910.0548
920.189
930.235
940.0266
950.00667
960.912
970.433
980.333
990.186



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: CNhs11772
library id: CNhs12996


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
0000061 (anatomical structure)
0000062 (organ)
0000160 (intestine)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001007 (digestive system)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002108 (small intestine)
0002114 (duodenum)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007026 (primitive gut)

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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