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FF:11801-124D1: 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 17:30, 29 March 2012


Name:CD14+CD16+ Monocytes, donor2
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 stageNA
sexmale
age23
cell typemonocyte
cell lineNA
companyNA
collaborationMichael Rehli (University of Regensberg)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number31
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-Peripheral0.0837
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-0.127
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.154
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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-Whole0.855
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: CNhs13208

Jaspar motifP-value
MA0002.26.44645e-9
MA0003.10.0589
MA0004.10.307
MA0006.10.868
MA0007.10.81
MA0009.10.319
MA0014.10.611
MA0017.10.0166
MA0018.20.0209
MA0019.10.736
MA0024.10.00656
MA0025.10.00162
MA0027.10.722
MA0028.10.627
MA0029.10.273
MA0030.10.364
MA0031.10.838
MA0035.20.51
MA0038.10.141
MA0039.20.598
MA0040.10.423
MA0041.10.841
MA0042.10.245
MA0043.12.3214e-6
MA0046.10.0364
MA0047.20.252
MA0048.10.741
MA0050.11.67455e-12
MA0051.11.47747e-6
MA0052.10.0469
MA0055.10.809
MA0057.10.704
MA0058.10.157
MA0059.10.282
MA0060.11.51884e-7
MA0061.18.79508e-9
MA0062.25.57393e-4
MA0065.20.00839
MA0066.10.0436
MA0067.14.6778e-5
MA0068.10.681
MA0069.10.472
MA0070.10.00704
MA0071.10.138
MA0072.10.784
MA0073.10.277
MA0074.10.197
MA0076.10.73
MA0077.10.0508
MA0078.10.832
MA0079.20.556
MA0080.21.06582e-15
MA0081.17.85842e-5
MA0083.10.77
MA0084.10.252
MA0087.10.24
MA0088.10.688
MA0090.10.0708
MA0091.10.684
MA0092.10.539
MA0093.10.358
MA0099.23.67016e-13
MA0100.10.761
MA0101.12.33384e-10
MA0102.27.97648e-10
MA0103.10.109
MA0104.20.282
MA0105.12.85255e-9
MA0106.10.638
MA0107.12.00756e-12
MA0108.24.29784e-5
MA0111.10.369
MA0112.23.00843e-4
MA0113.10.93
MA0114.10.101
MA0115.10.937
MA0116.11.10727e-4
MA0117.10.211
MA0119.10.466
MA0122.10.997
MA0124.10.392
MA0125.10.155
MA0131.10.94
MA0135.10.83
MA0136.15.87312e-19
MA0137.20.744
MA0138.20.681
MA0139.10.844
MA0140.10.408
MA0141.10.0309
MA0142.10.419
MA0143.10.791
MA0144.10.389
MA0145.10.274
MA0146.10.0539
MA0147.10.373
MA0148.10.71
MA0149.10.117
MA0150.12.27954e-6
MA0152.10.0962
MA0153.10.00323
MA0154.19.4701e-4
MA0155.10.721
MA0156.15.62848e-12
MA0157.10.556
MA0159.10.0415
MA0160.10.0157
MA0162.10.588
MA0163.11.52352e-10
MA0164.10.773
MA0258.10.012
MA0259.10.93



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: CNhs13208

Novel motifP-value
10.14
100.0245
1000.992
1010.753
1020.652
1030.262
1040.531
1050.126
1060.00534
1070.437
1080.707
1090.0479
110.183
1100.235
1110.0335
1120.226
1130.612
1140.014
1150.185
1160.956
1170.0289
1180.0852
1190.331
120.272
1200.7
1210.688
1220.596
1230.0291
1240.93
1250.147
1260.13
1270.33
1280.0909
1290.962
130.0784
1300.432
1310.831
1320.0339
1330.443
1340.686
1350.119
1360.739
1374.57357e-4
1380.245
1390.0493
140.41
1400.151
1410.65
1420.517
1430.123
1440.865
1450.554
1460.897
1470.46
1480.00904
1490.668
150.14
1500.504
1510.327
1520.215
1530.91
1540.897
1550.199
1560.949
1570.951
1580.0918
1590.416
160.413
1600.439
1610.422
1620.428
1630.933
1640.0934
1650.0461
1660.532
1670.134
1680.206
1690.0147
170.28
180.188
190.297
20.968
200.343
210.667
220.198
230.153
240.266
250.199
260.0702
270.792
280.551
290.0745
30.089
300.391
310.702
320.596
330.178
340.582
350.15
360.0487
370.0632
380.469
390.742
40.844
400.106
410.0223
420.349
430.0545
440.825
450.862
460.151
470.516
480.474
490.123
50.124
500.993
510.362
520.383
530.356
540.507
550.715
560.81
570.865
580.0704
590.112
60.886
600.0387
610.214
620.0292
630.518
640.375
650.253
660.15
670.316
680.527
690.7
70.168
700.0166
710.0358
720.223
730.121
740.044
750.0602
760.22
770.526
780.13
790.299
80.428
800.253
810.196
820.142
830.326
840.527
850.0455
860.107
870.253
880.51
890.452
90.253
900.255
910.448
920.526
930.506
940.0287
950.0595
960.319
970.856
980.0865
990.0254



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: CNhs13208


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)
0000040 (monoblast)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000557 (granulocyte monocyte progenitor cell)
0000559 (promonocyte)
0000566 (angioblastic mesenchymal cell)
0000576 (monocyte)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000763 (myeloid cell)
0000766 (myeloid leukocyte)
0000837 (hematopoietic multipotent progenitor cell)
0000839 (myeloid lineage restricted progenitor cell)
0000860 (classical monocyte)
0000988 (hematopoietic cell)
0001012 (CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor)
0002009 (macrophage dendritic cell progenitor)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002057 (CD14-positive, CD16-negative classical monocyte)
0002087 (nongranular leukocyte)
0002194 (monopoietic cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002393 (intermediate monocyte)
0002397 (CD14-positive, CD16-positive monocyte)

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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