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FF:11912-125G4: 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 17:37, 29 March 2012


Name:CD14+CD16+ Monocytes, donor3
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 number45-46
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-Peripheral0.0827
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-0.132
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.0827
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-Whole0.741
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: CNhs13549

Jaspar motifP-value
MA0002.21.97897e-9
MA0003.10.0746
MA0004.10.276
MA0006.10.798
MA0007.10.937
MA0009.10.446
MA0014.10.442
MA0017.10.00843
MA0018.20.022
MA0019.10.733
MA0024.10.00635
MA0025.16.12069e-5
MA0027.10.729
MA0028.10.428
MA0029.10.176
MA0030.10.243
MA0031.10.539
MA0035.20.505
MA0038.10.394
MA0039.20.432
MA0040.10.269
MA0041.10.924
MA0042.10.139
MA0043.19.58836e-7
MA0046.10.0416
MA0047.20.133
MA0048.10.839
MA0050.11.83373e-12
MA0051.13.27243e-6
MA0052.10.0235
MA0055.10.77
MA0057.10.681
MA0058.10.127
MA0059.10.247
MA0060.17.50323e-6
MA0061.13.64207e-8
MA0062.24.61845e-5
MA0065.20.00668
MA0066.10.0458
MA0067.12.70449e-5
MA0068.10.773
MA0069.10.738
MA0070.10.00379
MA0071.10.123
MA0072.10.526
MA0073.10.37
MA0074.10.318
MA0076.10.356
MA0077.10.0938
MA0078.10.986
MA0079.20.499
MA0080.21.28657e-15
MA0081.16.19081e-5
MA0083.10.845
MA0084.10.372
MA0087.10.357
MA0088.10.653
MA0090.10.0428
MA0091.10.698
MA0092.10.574
MA0093.10.309
MA0099.25.7304e-11
MA0100.10.9
MA0101.16.47375e-9
MA0102.23.8747e-9
MA0103.10.123
MA0104.20.196
MA0105.13.25902e-9
MA0106.10.71
MA0107.11.34901e-10
MA0108.27.9364e-5
MA0111.10.452
MA0112.22.43821e-4
MA0113.10.846
MA0114.10.0614
MA0115.10.867
MA0116.11.58021e-4
MA0117.10.173
MA0119.10.458
MA0122.10.823
MA0124.10.266
MA0125.10.235
MA0131.10.987
MA0135.10.446
MA0136.16.89987e-19
MA0137.20.404
MA0138.20.839
MA0139.10.911
MA0140.10.57
MA0141.10.0187
MA0142.10.442
MA0143.10.841
MA0144.10.272
MA0145.10.204
MA0146.10.0736
MA0147.10.276
MA0148.10.393
MA0149.10.106
MA0150.18.53738e-6
MA0152.10.189
MA0153.10.00876
MA0154.10.00166
MA0155.10.762
MA0156.13.71559e-13
MA0157.10.286
MA0159.10.0352
MA0160.10.00728
MA0162.10.505
MA0163.14.07237e-10
MA0164.10.929
MA0258.10.00968
MA0259.10.833



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: CNhs13549

Novel motifP-value
10.133
100.03
1000.887
1010.609
1020.649
1030.298
1040.535
1050.147
1060.00917
1070.665
1080.672
1090.049
110.214
1100.195
1110.0506
1120.28
1130.438
1140.0154
1150.119
1160.985
1170.0292
1180.107
1190.421
120.292
1200.777
1210.716
1220.581
1230.0303
1240.622
1250.216
1260.122
1270.374
1280.0757
1290.997
130.0616
1300.288
1310.826
1320.0262
1330.491
1340.73
1350.089
1360.739
1371.15479e-4
1380.272
1390.0652
140.393
1400.228
1410.506
1420.465
1430.0733
1440.846
1450.572
1460.996
1470.596
1480.0141
1490.812
150.13
1500.603
1510.354
1520.288
1530.855
1540.806
1550.251
1560.877
1570.889
1580.12
1590.209
160.465
1600.422
1610.438
1620.343
1630.802
1640.1
1650.0729
1660.677
1670.185
1680.266
1690.012
170.263
180.175
190.349
20.867
200.437
210.662
220.218
230.222
240.245
250.171
260.0472
270.686
280.503
290.0897
30.104
300.434
310.679
320.575
330.161
340.572
350.182
360.0289
370.0618
380.469
390.809
40.729
400.0592
410.0195
420.312
430.0744
440.899
450.911
460.172
470.522
480.496
490.142
50.103
500.978
510.381
520.386
530.315
540.509
550.65
560.873
570.864
580.0754
590.188
60.703
600.0464
610.272
620.0342
630.534
640.353
650.32
660.215
670.318
680.68
690.918
70.134
700.0258
710.0258
720.2
730.121
740.0975
750.0692
760.213
770.607
780.161
790.423
80.429
800.167
810.233
820.24
830.15
840.68
850.0394
860.126
870.204
880.576
890.476
90.281
900.132
910.396
920.465
930.291
940.0225
950.0615
960.446
970.838
980.0915
990.0239



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: CNhs13549


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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