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FF:11224-116B9: 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:CD14+ Monocytes, 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 stage47 years old adult
sexmale
age47
cell typemonocyte
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberMon725
catalog number3H100-30-10
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-Peripheral0.576
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-0.0916
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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-Whole0.208
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-Whole0.191
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: CNhs10852

Jaspar motifP-value
MA0002.22.99369e-9
MA0003.10.825
MA0004.10.585
MA0006.10.676
MA0007.10.956
MA0009.10.205
MA0014.10.964
MA0017.10.553
MA0018.20.00752
MA0019.10.36
MA0024.10.0103
MA0025.13.85989e-4
MA0027.10.782
MA0028.10.0649
MA0029.10.135
MA0030.10.563
MA0031.10.588
MA0035.20.238
MA0038.10.85
MA0039.20.766
MA0040.10.566
MA0041.10.715
MA0042.10.801
MA0043.17.53342e-11
MA0046.10.00557
MA0047.20.897
MA0048.10.518
MA0050.11.39456e-7
MA0051.14.47201e-4
MA0052.10.00367
MA0055.10.312
MA0057.10.252
MA0058.10.445
MA0059.10.667
MA0060.12.8654e-7
MA0061.17.50286e-32
MA0062.20.103
MA0065.20.151
MA0066.10.0868
MA0067.11.11026e-6
MA0068.10.555
MA0069.10.705
MA0070.10.026
MA0071.10.276
MA0072.10.4
MA0073.10.303
MA0074.10.124
MA0076.10.168
MA0077.10.265
MA0078.10.606
MA0079.20.223
MA0080.22.15277e-12
MA0081.14.12756e-4
MA0083.10.704
MA0084.10.946
MA0087.10.945
MA0088.10.258
MA0090.10.319
MA0091.10.608
MA0092.10.426
MA0093.10.703
MA0099.21.21327e-46
MA0100.10.705
MA0101.13.04487e-31
MA0102.21.503e-10
MA0103.10.0114
MA0104.20.441
MA0105.14.18875e-30
MA0106.10.344
MA0107.11.61202e-37
MA0108.20.149
MA0111.10.681
MA0112.20.0048
MA0113.10.845
MA0114.10.782
MA0115.10.226
MA0116.10.00219
MA0117.10.0114
MA0119.10.351
MA0122.10.94
MA0124.10.553
MA0125.10.129
MA0131.10.777
MA0135.10.556
MA0136.11.84649e-13
MA0137.20.493
MA0138.20.017
MA0139.10.171
MA0140.10.176
MA0141.10.274
MA0142.10.917
MA0143.10.732
MA0144.10.246
MA0145.10.661
MA0146.10.762
MA0147.10.603
MA0148.10.571
MA0149.10.413
MA0150.11.62974e-20
MA0152.10.37
MA0153.10.00744
MA0154.11.92985e-4
MA0155.10.738
MA0156.13.47618e-10
MA0157.10.384
MA0159.10.0798
MA0160.10.117
MA0162.10.837
MA0163.15.70376e-5
MA0164.10.653
MA0258.10.0527
MA0259.10.685



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: CNhs10852

Novel motifP-value
10.31
100.0233
1000.766
1010.946
1020.827
1030.603
1040.452
1050.0501
1060.00146
1070.322
1080.492
1090.476
110.445
1100.354
1110.13
1120.651
1130.176
1140.145
1150.0813
1160.798
1170.0989
1180.224
1190.512
120.241
1200.354
1210.629
1220.604
1230.0112
1240.861
1250.375
1260.263
1270.825
1280.11
1290.846
130.125
1300.33
1310.835
1320.0528
1330.595
1340.857
1350.679
1360.897
1370.0164
1380.34
1390.0711
140.363
1400.583
1410.464
1420.198
1430.0294
1440.607
1450.533
1460.954
1470.619
1480.069
1490.74
150.166
1500.548
1510.219
1520.345
1530.861
1540.545
1550.637
1560.64
1570.724
1580.0606
1590.122
160.803
1600.934
1610.823
1620.116
1630.13
1640.0859
1650.291
1660.7
1670.267
1680.0688
1690.109
170.395
180.253
190.969
20.278
200.278
210.903
220.485
230.0509
240.667
250.393
260.129
270.41
280.412
290.31
30.301
300.234
310.832
320.106
330.27
340.685
350.163
360.0666
370.155
380.41
390.769
40.754
400.176
410.00808
420.451
430.0276
440.278
450.921
460.408
470.984
480.844
490.11
50.244
500.979
510.537
520.464
530.235
540.596
550.93
560.934
570.897
580.242
590.599
60.955
600.086
610.51
620.169
630.655
640.591
650.273
660.0948
670.644
680.286
690.225
70.263
700.0969
710.0504
720.234
730.238
740.0289
750.264
760.0689
770.921
780.304
790.75
80.978
800.0832
810.368
820.335
830.163
840.0436
850.137
860.0545
870.57
880.833
890.887
90.428
900.292
910.259
920.42
930.621
940.0964
950.312
960.479
970.611
980.118
990.00815



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: CNhs10852


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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