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FF:11228-116C4: 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 16:34, 29 March 2012


Name:Dendritic Cells - plasmacytoid, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stage22 years old adult
sexfemale
age22
cell typedendritic cell, plasmacytoid
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberPDC737
catalog number3H100-72-5
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
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-penis-0.143
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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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: CNhs10857

Jaspar motifP-value
MA0002.22.87346e-8
MA0003.10.933
MA0004.10.332
MA0006.10.575
MA0007.10.73
MA0009.10.109
MA0014.10.794
MA0017.10.887
MA0018.20.00319
MA0019.10.542
MA0024.10.077
MA0025.10.0798
MA0027.10.433
MA0028.10.257
MA0029.10.706
MA0030.10.441
MA0031.10.191
MA0035.20.523
MA0038.10.148
MA0039.20.575
MA0040.10.948
MA0041.10.293
MA0042.10.793
MA0043.14.07063e-4
MA0046.10.142
MA0047.20.624
MA0048.10.00561
MA0050.11.65798e-4
MA0051.10.0244
MA0052.10.182
MA0055.13.39387e-4
MA0057.10.278
MA0058.10.205
MA0059.10.437
MA0060.10.0433
MA0061.15.27558e-14
MA0062.27.95191e-8
MA0065.20.398
MA0066.10.376
MA0067.17.84337e-4
MA0068.10.133
MA0069.10.804
MA0070.10.0356
MA0071.10.663
MA0072.10.502
MA0073.10.349
MA0074.10.621
MA0076.10.043
MA0077.10.315
MA0078.10.939
MA0079.20.977
MA0080.22.53396e-13
MA0081.11.4981e-5
MA0083.10.216
MA0084.10.736
MA0087.10.748
MA0088.10.985
MA0090.19.6346e-4
MA0091.10.0817
MA0092.10.933
MA0093.10.404
MA0099.21.02178e-6
MA0100.10.884
MA0101.11.44128e-14
MA0102.22.27259e-4
MA0103.10.095
MA0104.20.0791
MA0105.13.9674e-10
MA0106.10.075
MA0107.15.67079e-16
MA0108.22.0596e-4
MA0111.10.227
MA0112.20.265
MA0113.10.978
MA0114.10.618
MA0115.10.0719
MA0116.10.00318
MA0117.10.0806
MA0119.10.828
MA0122.10.806
MA0124.10.9
MA0125.10.231
MA0131.10.676
MA0135.10.19
MA0136.11.09579e-14
MA0137.20.491
MA0138.20.404
MA0139.10.735
MA0140.10.643
MA0141.10.838
MA0142.10.823
MA0143.10.941
MA0144.10.976
MA0145.10.26
MA0146.10.252
MA0147.10.109
MA0148.10.338
MA0149.10.707
MA0150.16.14971e-5
MA0152.10.0775
MA0153.13.87981e-4
MA0154.10.00836
MA0155.10.466
MA0156.11.42717e-11
MA0157.10.239
MA0159.10.396
MA0160.10.875
MA0162.10.56
MA0163.11.89354e-4
MA0164.10.665
MA0258.10.141
MA0259.10.484



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: CNhs10857

Novel motifP-value
10.322
100.0136
1000.954
1010.493
1020.557
1030.228
1040.366
1050.342
1060.00918
1070.778
1080.17
1090.191
110.278
1100.697
1110.135
1120.763
1130.582
1140.121
1150.505
1160.877
1170.00627
1180.239
1190.173
120.414
1200.892
1210.423
1220.186
1230.00319
1240.207
1250.0627
1260.483
1270.603
1280.13
1290.956
130.066
1300.949
1310.969
1320.0561
1330.341
1340.455
1350.916
1360.547
1370.00166
1380.642
1390.0381
140.192
1400.996
1410.421
1420.348
1430.011
1440.817
1450.754
1460.776
1470.148
1480.024
1490.499
150.0723
1500.586
1510.274
1520.994
1530.454
1540.458
1550.0703
1560.921
1570.745
1580.163
1590.231
160.738
1600.681
1610.744
1620.647
1630.672
1640.233
1650.215
1660.331
1670.177
1680.734
1690.951
170.915
180.636
190.381
20.491
200.911
210.847
220.999
230.468
240.371
250.198
260.349
270.548
280.408
290.0202
30.133
300.141
310.736
320.042
330.206
340.966
350.0475
360.128
370.095
380.528
390.722
40.421
400.674
410.05
420.0813
430.104
440.978
450.533
460.379
470.551
480.687
490.105
50.476
500.753
510.382
520.586
530.32
540.83
550.604
560.513
570.586
580.0526
590.888
60.563
600.19
610.0739
620.0277
630.65
640.463
650.671
660.419
670.291
680.367
690.718
70.175
700.0282
710.0631
720.229
730.553
740.252
750.0773
760.324
770.719
780.0362
790.937
80.753
800.121
810.315
820.242
830.284
840.033
850.221
860.0643
870.121
880.45
890.473
90.692
900.0691
910.842
920.526
930.508
940.0937
950.153
960.923
970.936
980.228
996.13711e-4



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: CNhs10857


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000451 (dendritic cell)
0000548 (animal cell)
0000557 (granulocyte monocyte progenitor cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000763 (myeloid cell)
0000784 (plasmacytoid dendritic cell)
0000837 (hematopoietic multipotent progenitor cell)
0000840 (immature conventional dendritic cell)
0000988 (hematopoietic cell)
0000990 (conventional dendritic cell)
0001012 (CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor)
0001019 (CD115-positive monocyte OR common dendritic progenitor)
0001029 (common dendritic progenitor)
0002009 (macrophage dendritic cell progenitor)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
0005423 (developing anatomical structure)

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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