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FF:10077-102A5: 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 16:53, 29 March 2012


Name:lymph node, adult, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuelymph node
dev stage30 years old adult
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyAmbion
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number8060051
catalog numberCat:AM7894
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-ToTALLY-RNA-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-penis0.122
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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-Whole0.175
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: CNhs11788

Jaspar motifP-value
MA0002.22.04732e-5
MA0003.10.0856
MA0004.10.871
MA0006.10.274
MA0007.10.112
MA0009.10.486
MA0014.10.299
MA0017.10.00138
MA0018.23.30068e-4
MA0019.10.971
MA0024.10.054
MA0025.10.0782
MA0027.10.722
MA0028.10.104
MA0029.10.419
MA0030.10.711
MA0031.10.213
MA0035.20.519
MA0038.10.0315
MA0039.20.914
MA0040.10.994
MA0041.10.573
MA0042.10.747
MA0043.16.60967e-4
MA0046.10.159
MA0047.20.561
MA0048.10.0539
MA0050.11.02635e-9
MA0051.12.78112e-4
MA0052.10.526
MA0055.10.00507
MA0057.10.212
MA0058.10.764
MA0059.10.489
MA0060.13.58096e-6
MA0061.10.253
MA0062.20.191
MA0065.20.0222
MA0066.10.435
MA0067.10.235
MA0068.10.298
MA0069.10.802
MA0070.10.973
MA0071.10.739
MA0072.10.0492
MA0073.10.919
MA0074.10.716
MA0076.10.185
MA0077.10.487
MA0078.10.557
MA0079.20.0493
MA0080.26.34184e-17
MA0081.10.0054
MA0083.10.568
MA0084.10.495
MA0087.10.617
MA0088.10.309
MA0090.10.039
MA0091.10.183
MA0092.10.58
MA0093.10.61
MA0099.21.85498e-25
MA0100.10.159
MA0101.10.814
MA0102.20.153
MA0103.10.0361
MA0104.20.0768
MA0105.10.427
MA0106.10.0125
MA0107.10.963
MA0108.20.156
MA0111.10.262
MA0112.20.0136
MA0113.10.0271
MA0114.10.156
MA0115.10.61
MA0116.10.002
MA0117.10.0315
MA0119.10.707
MA0122.10.541
MA0124.10.34
MA0125.10.211
MA0131.10.355
MA0135.10.972
MA0136.13.69753e-13
MA0137.20.00215
MA0138.20.12
MA0139.10.748
MA0140.10.893
MA0141.10.63
MA0142.10.838
MA0143.10.965
MA0144.10.00576
MA0145.10.434
MA0146.10.0458
MA0147.10.121
MA0148.10.504
MA0149.10.884
MA0150.10.00289
MA0152.10.33
MA0153.10.0347
MA0154.10.0479
MA0155.10.0731
MA0156.12.98337e-11
MA0157.10.104
MA0159.10.657
MA0160.10.456
MA0162.10.595
MA0163.10.0919
MA0164.10.423
MA0258.10.0599
MA0259.10.0531



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: CNhs11788

Novel motifP-value
10.964
100.643
1000.507
1010.398
1020.983
1030.379
1040.94
1050.211
1064.93633e-4
1070.0038
1080.602
1090.578
110.193
1100.779
1110.317
1120.057
1130.00518
1140.785
1150.539
1160.989
1170.664
1180.671
1190.359
120.399
1200.23
1210.613
1220.988
1230.272
1240.482
1250.216
1260.363
1270.259
1280.0636
1290.159
130.296
1300.403
1310.285
1320.107
1330.0695
1340.777
1350.0379
1360.309
1370.292
1380.27
1390.139
140.313
1400.889
1410.345
1420.328
1430.11
1440.564
1450.0599
1460.738
1470.298
1480.1
1490.0338
150.666
1500.278
1510.564
1520.0727
1530.337
1540.715
1550.191
1560.583
1570.482
1580.751
1590.775
160.918
1600.461
1610.878
1620.644
1630.154
1640.974
1650.345
1660.966
1670.345
1680.0118
1690.0061
170.608
180.993
190.191
20.031
200.197
210.483
220.19
230.425
240.728
250.736
260.3
270.00175
280.633
290.851
30.128
300.644
310.407
320.868
330.302
340.0917
350.436
360.878
370.825
380.722
390.742
40.426
400.859
410.45
420.602
430.254
440.0235
450.208
460.314
470.944
480.313
490.236
50.958
500.304
510.613
520.313
530.0963
540.395
550.276
560.954
570.555
580.187
590.0921
60.438
600.0428
610.175
620.198
630.533
640.743
650.234
660.0282
670.499
680.404
690.564
70.745
700.732
710.499
720.0504
730.426
740.403
750.852
760.733
770.124
780.164
790.107
80.211
800.00524
810.442
820.0336
830.123
840.154
850.148
860.237
870.626
880.533
890.863
90.165
900.881
910.183
920.114
930.255
940.726
950.701
960.922
970.41
980.842
990.811



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: CNhs11788


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
0000029 (lymph node)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0001062 (anatomical entity)
0002193 (hemolymphoid system)
0002405 (immune system)
0002465 (lymphoid system)
0007023 (adult organism)

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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