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FF:11874-125C2: 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 17:36, 29 March 2012


Name:CD14+ monocytes - treated with Group A streptococci, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexmale
age51
cell typemonocyte
cell lineNA
companyNA
collaborationChristine Wells (University of Queensland)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberD4-5
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-Peripheral1.013
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
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C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
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-Whole0.215
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: CNhs13532

Jaspar motifP-value
MA0002.24.47736e-9
MA0003.10.805
MA0004.10.297
MA0006.10.839
MA0007.10.785
MA0009.10.588
MA0014.10.707
MA0017.10.18
MA0018.20.0535
MA0019.10.796
MA0024.10.00469
MA0025.15.91862e-4
MA0027.10.979
MA0028.10.117
MA0029.10.231
MA0030.10.232
MA0031.10.354
MA0035.20.347
MA0038.10.722
MA0039.20.64
MA0040.10.747
MA0041.10.604
MA0042.10.797
MA0043.11.93608e-8
MA0046.10.0203
MA0047.20.324
MA0048.10.75
MA0050.13.54954e-11
MA0051.12.42576e-5
MA0052.10.0347
MA0055.10.611
MA0057.10.401
MA0058.10.11
MA0059.10.146
MA0060.11.19301e-8
MA0061.13.60428e-16
MA0062.20.659
MA0065.20.0396
MA0066.10.0296
MA0067.12.17271e-6
MA0068.10.71
MA0069.10.817
MA0070.10.0313
MA0071.10.428
MA0072.10.553
MA0073.10.386
MA0074.10.149
MA0076.10.168
MA0077.10.266
MA0078.10.372
MA0079.20.129
MA0080.22.94564e-11
MA0081.13.70671e-4
MA0083.10.811
MA0084.10.597
MA0087.10.702
MA0088.10.488
MA0090.10.566
MA0091.10.668
MA0092.10.302
MA0093.10.327
MA0099.22.84712e-44
MA0100.10.858
MA0101.13.15037e-17
MA0102.26.92804e-9
MA0103.10.0268
MA0104.20.288
MA0105.13.09649e-21
MA0106.10.814
MA0107.17.19224e-22
MA0108.20.448
MA0111.10.47
MA0112.22.90208e-4
MA0113.11
MA0114.10.256
MA0115.10.765
MA0116.12.24332e-4
MA0117.10.0398
MA0119.10.232
MA0122.10.607
MA0124.10.245
MA0125.10.29
MA0131.10.358
MA0135.10.276
MA0136.16.03247e-12
MA0137.20.13
MA0138.20.292
MA0139.10.654
MA0140.10.384
MA0141.10.199
MA0142.10.608
MA0143.10.966
MA0144.10.0817
MA0145.10.598
MA0146.10.814
MA0147.10.388
MA0148.10.729
MA0149.10.182
MA0150.15.63344e-22
MA0152.10.731
MA0153.10.00428
MA0154.19.93587e-5
MA0155.10.924
MA0156.11.82119e-8
MA0157.10.863
MA0159.10.027
MA0160.10.0733
MA0162.10.83
MA0163.13.29622e-7
MA0164.10.643
MA0258.10.0283
MA0259.10.774



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: CNhs13532

Novel motifP-value
10.119
100.0279
1000.797
1010.764
1020.965
1030.244
1040.568
1050.109
1060.0012
1070.206
1080.556
1090.417
110.209
1100.212
1110.159
1120.298
1130.486
1140.0345
1150.253
1160.969
1170.119
1180.198
1190.184
120.314
1200.794
1210.524
1220.592
1230.73
1240.557
1250.344
1260.234
1270.467
1280.0523
1290.37
130.118
1300.401
1310.849
1320.0423
1330.582
1340.508
1350.802
1360.842
1370.0278
1380.384
1390.117
140.509
1400.545
1410.272
1420.0326
1430.0238
1440.445
1450.414
1460.853
1470.738
1480.0131
1490.944
150.165
1500.373
1510.523
1520.395
1530.558
1540.801
1550.919
1560.935
1570.556
1580.0412
1590.139
160.406
1600.451
1610.486
1620.161
1630.13
1640.16
1650.308
1660.736
1670.33
1680.144
1690.0243
170.273
180.0874
190.526
20.486
200.232
210.828
220.326
230.034
240.408
250.487
260.0939
270.507
280.396
290.296
30.167
300.49
310.767
320.388
330.272
340.754
350.137
360.0697
370.0798
380.37
390.826
40.869
400.26
410.0176
420.354
430.0214
440.579
450.768
460.22
470.662
480.601
490.129
50.296
500.964
510.497
520.455
530.72
540.483
550.534
560.687
570.87
580.163
590.243
60.896
600.0604
610.681
620.0927
630.619
640.491
650.234
660.236
670.491
680.671
690.384
70.249
700.0653
710.0299
720.116
730.239
740.0517
750.195
760.17
770.634
780.138
790.663
80.433
800.144
810.333
820.232
830.0154
840.14
850.0303
860.0656
870.504
880.714
890.209
90.337
900.117
910.441
920.298
930.411
940.0957
950.522
960.381
970.522
980.179
990.052



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: CNhs13532


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)

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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