FF:11736-123E8: Difference between revisions

Latest revision as of 18:16, 4 June 2020

Name:	Mouse Microglia, donor2
Species:	Mouse (Mus musculus)
Library ID:	CNhs12634
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	brain
dev stage	NA
sex	NA
age	NA
cell type	microglial cell
cell line	NA
company	Sciencell/3H
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	RNAMG2
catalog number	custom
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005410

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12634		CAGE		DRX008829		DRR009701

Accession ID Mm9

Library id		BAM		CTSS
CNhs12634		DRZ001126		DRZ002511

Accession ID Mm10

Library id		BAM		CTSS
CNhs12634		DRZ012476		DRZ013861

Download raw sequence, BAM & CTSS

Mm9

Fasta	BAM	CTSS
download	download	donwload

Mm10

BAM	CTSS
download	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. Analyst:NA link to dataset. data

CNhs12634

0	0
1	0
10	0
100	0
1000	0.664
1001	-0.0749
1002	0.0639
1003	0.583
1004	0
1005	0
1006	0.256
1007	-0.229
1008	0
1009	0.0576
101	-0.552
1010	0
1011	0.0337
1012	0
1013	0.117
1014	0
1015	0.256
1016	0.213
1017	0
1018	0
1019	0
102	0
1020	0.61
1021	0.141
1022	0.012
1023	0
1024	-0.156
1025	-0.0196
1026	0
1027	0.405
1028	0.141
1029	-0.176
103	0.164
1030	0
1031	0.403
1032	0.756
1033	-0.0665
1034	0
1035	0
1036	-0.183
1037	0
1038	-0.217
1039	0.127
104	0
1040	0.283
1041	0

Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed. Analyst:NA link to dataset. data

TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifsSummary: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 Analyst: Michiel de Hoon link to dataset. data

library id: CNhs12634

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.621
MA0003.1	MA0003.1	0.153
MA0004.1	MA0004.1	0.383
MA0006.1	MA0006.1	0.405
MA0007.1	MA0007.1	0.61
MA0009.1	MA0009.1	0.159
MA0014.1	MA0014.1	0.787
MA0017.1	MA0017.1	9.73702e-4
MA0018.2	MA0018.2	0.586
MA0019.1	MA0019.1	0.23
MA0024.1	MA0024.1	0.00289
MA0025.1	MA0025.1	0.837
MA0027.1	MA0027.1	0.245
MA0028.1	MA0028.1	5.23907e-4
MA0029.1	MA0029.1	0.656
MA0030.1	MA0030.1	0.677
MA0031.1	MA0031.1	0.601
MA0035.2	MA0035.2	0.00184
MA0038.1	MA0038.1	0.0678
MA0039.2	MA0039.2	0.928
MA0040.1	MA0040.1	0.47
MA0041.1	MA0041.1	0.258
MA0042.1	MA0042.1	0.726
MA0043.1	MA0043.1	0.936
MA0046.1	MA0046.1	2.79439e-6
MA0047.2	MA0047.2	0.106
MA0048.1	MA0048.1	0.443
MA0050.1	MA0050.1	0.34
MA0051.1	MA0051.1	0.81
MA0052.1	MA0052.1	0.34
MA0055.1	MA0055.1	0.652
MA0057.1	MA0057.1	0.682
MA0058.1	MA0058.1	0.589
MA0059.1	MA0059.1	0.946
MA0060.1	MA0060.1	0.985
MA0061.1	MA0061.1	0.601
MA0062.2	MA0062.2	3.25868e-6
MA0065.2	MA0065.2	0.833
MA0066.1	MA0066.1	0.616
MA0067.1	MA0067.1	0.185
MA0068.1	MA0068.1	0.598
MA0069.1	MA0069.1	0.211
MA0070.1	MA0070.1	0.368
MA0071.1	MA0071.1	0.301
MA0072.1	MA0072.1	0.321
MA0073.1	MA0073.1	0.921
MA0074.1	MA0074.1	0.227
MA0076.1	MA0076.1	0.00129
MA0077.1	MA0077.1	0.372
MA0078.1	MA0078.1	0.548
MA0079.2	MA0079.2	0.0146
MA0080.2	MA0080.2	0.0695
MA0081.1	MA0081.1	0.754
MA0083.1	MA0083.1	0.975
MA0084.1	MA0084.1	0.374
MA0087.1	MA0087.1	0.955
MA0088.1	MA0088.1	0.552
MA0090.1	MA0090.1	0.914
MA0091.1	MA0091.1	0.307
MA0092.1	MA0092.1	0.805
MA0093.1	MA0093.1	0.438
MA0099.2	MA0099.2	0.675
MA0100.1	MA0100.1	0.627
MA0101.1	MA0101.1	0.332
MA0102.2	MA0102.2	0.214
MA0103.1	MA0103.1	0.123
MA0104.2	MA0104.2	0.429
MA0105.1	MA0105.1	0.815
MA0106.1	MA0106.1	0.424
MA0107.1	MA0107.1	0.413
MA0108.2	MA0108.2	0.367
MA0111.1	MA0111.1	0.529
MA0112.2	MA0112.2	0.751
MA0113.1	MA0113.1	0.864
MA0114.1	MA0114.1	0.00386
MA0115.1	MA0115.1	0.0212
MA0116.1	MA0116.1	0.709
MA0117.1	MA0117.1	0.539
MA0119.1	MA0119.1	0.616
MA0122.1	MA0122.1	0.872
MA0124.1	MA0124.1	0.778
MA0125.1	MA0125.1	0.637
MA0131.1	MA0131.1	0.0957
MA0135.1	MA0135.1	0.0752
MA0136.1	MA0136.1	0.0266
MA0137.2	MA0137.2	0.428
MA0138.2	MA0138.2	0.58
MA0139.1	MA0139.1	0.642
MA0140.1	MA0140.1	3.80558e-5
MA0141.1	MA0141.1	0.814
MA0142.1	MA0142.1	0.8
MA0143.1	MA0143.1	0.827
MA0144.1	MA0144.1	0.203
MA0145.1	MA0145.1	0.136
MA0146.1	MA0146.1	0.0408
MA0147.1	MA0147.1	0.473
MA0148.1	MA0148.1	0.0258
MA0149.1	MA0149.1	0.191
MA0150.1	MA0150.1	0.23
MA0152.1	MA0152.1	0.076
MA0153.1	MA0153.1	4.93809e-4
MA0154.1	MA0154.1	0.205
MA0155.1	MA0155.1	0.085
MA0156.1	MA0156.1	6.7189e-5
MA0157.1	MA0157.1	0.478
MA0159.1	MA0159.1	0.776
MA0160.1	MA0160.1	0.141
MA0162.1	MA0162.1	0.351
MA0163.1	MA0163.1	0.114
MA0164.1	MA0164.1	0.823
MA0258.1	MA0258.1	0.975
MA0259.1	MA0259.1	0.132

FANTOM5 phase1 novel unique motifsSummary: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 Analyst: Michiel de Hoon link to dataset. data

library id: CNhs12634

Novel motif	Logo	P-value
1	1	0.318
10	10	0.471
100	100	0.996
101	101	0.984
102	102	0.75
103	103	0.222
104	104	0.94
105	105	0.893
106	106	0.098
107	107	0.947
108	108	0.29
109	109	0.266
11	11	0.814
110	110	0.738
111	111	0.594
112	112	0.407
113	113	0.411
114	114	0.88
115	115	0.801
116	116	0.126
117	117	0.14
118	118	0.675
119	119	0.126
12	12	0.917
120	120	0.316
121	121	0.591
122	122	0.567
123	123	0.728
124	124	0.952
125	125	0.114
126	126	0.42
127	127	0.97
128	128	0.592
129	129	0.119
13	13	0.101
130	130	0.837
131	131	0.771
132	132	0.109
133	133	0.826
134	134	0.744
135	135	0.103
136	136	0.0506
137	137	0.423
138	138	0.525
139	139	0.039
14	14	0.326
140	140	0.0583
141	141	0.257
142	142	0.0231
143	143	0.855
144	144	0.837
145	145	0.118
146	146	0.631
147	147	0.94
148	148	0.861
149	149	0.148
15	15	0.205
150	150	0.307
151	151	0.312
152	152	0.0404
153	153	0.13
154	154	0.0611
155	155	0.816
156	156	0.0164
157	157	0.335
158	158	0.0168
159	159	0.218
160	160	0.622
161	161	0.559
162	162	0.584
163	163	0.152
164	164	3.20609e-4
165	165	0.992
166	166	0.981
167	167	0.0431
168	168	0.605
169	169	0.268
17	17	0.653
18	18	0.804
19	19	0.619
2	2	0.0258
20	20	0.76
21	21	0.44
22	22	0.175
23	23	0.129
24	24	0.592
25	25	0.167
26	26	0.729
27	27	0.528
28	28	0.314
29	29	0.127
3	3	0.696
30	30	0.105
31	31	0.315
32	32	0.00711
33	33	0.7
34	34	0.0296
35	35	0.492
36	36	0.55
37	37	0.576
38	38	0.55
39	39	0.434
4	4	0.862
40	40	0.544
41	41	0.815
42	42	0.665
43	43	0.51
44	44	0.313
45	45	0.179
46	46	0.41
47	47	0.872
48	48	0.918
49	49	0.366
5	5	0.0567
50	50	0.179
51	51	0.777
52	52	0.0736
53	53	0.762
54	54	0.635
55	55	0.366
56	56	0.391
57	57	0.549
58	58	0.182
59	59	0.00895
6	6	0.993
60	60	0.371
61	61	0.418
62	62	0.398
63	63	0.174
64	64	0.762
65	65	0.0785
66	66	0.626
67	67	0.663
68	68	0.254
69	69	0.0994
7	7	0.0476
70	70	0.984
71	71	0.593
72	72	0.785
73	73	0.0762
74	74	0.348
75	75	0.64
76	76	0.116
77	77	0.00817
78	78	0.00452
79	79	0.865
8	8	0.596
80	80	0.547
81	81	0.369
82	82	0.421
83	83	0.481
84	84	0.417
85	85	0.468
86	86	0.86
87	87	0.00126
88	88	0.266
89	89	0.685
9	9	0.735
90	90	0.191
91	91	0.815
92	92	0.396
93	93	0.0887
94	94	0.0157
95	95	0.197
96	96	0.11
97	97	0.895
98	98	0.2
99	99	0.204

de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown. Analyst:NA library id: CNhs12634

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000113 mouse microglial cell sample

Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship Analyst: Hideya Kawaji link to source data data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000988 (hematopoietic cell)
0000548 (animal cell)
0000763 (myeloid cell)
0002371 (somatic cell)
0000766 (myeloid leukocyte)
0002319 (neural cell)
0000095 (neuron associated cell)
0000243 (glial cell (sensu Vertebrata))
0000878 (central nervous system macrophage)
0000219 (motile cell)
0000325 (stuff accumulating cell)
0000473 (defensive cell)
0000234 (phagocyte)
0000125 (glial cell)
0000738 (leukocyte)
0000255 (eukaryotic cell)
0000235 (macrophage)
0000864 (tissue-resident macrophage)
0000129 (microglial cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0011216 (organ system subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000113 (mouse microglial cell sample)

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship Analyst: Hideya Kawaji link to source data data
CL:0000133 (neurectodermal cell)
CL:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)
CL:0000339 (glioblast (sensu Vertebrata))
CL:0000221 (ectodermal cell)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002371,UBERON:0001474,UBERON:0002384,UBERON:0000926,UBERON:0000479,UBERON:0000073,UBERON:0004121,UBERON:0000062,UBERON:0004765,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0000467,UBERON:0001062,UBERON:0005291,UBERON:0006598,UBERON:0002532,UBERON:0001017,UBERON:0001016,UBERON:0002204,UBERON:0001434,UBERON:0000924,UBERON:0002390,UBERON:0005743,UBERON:0002193,UBERON:0002405,UBERON:0003081,UBERON:0006601,UBERON:0006603,UBERON:0003061
+|DRA_sample_Accession=CAGE@SAMD00005410
-|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000333,CL:0000055,CL:0000144,CL:0000723,CL:0000048,CL:0000988,CL:0000839,CL:0000548,CL:0002194,CL:0000034,CL:0002032,CL:0000763,CL:0000012,CL:0002321,CL:0002320,CL:0000063,CL:0002371,CL:0000864,CL:0000766,CL:0002319,CL:0000221,CL:0000095,CL:0000243,CL:0000878,CL:0000219,CL:0000220,CL:0000123,CL:0000125,CL:0000004,CL:0000134,CL:0000030,CL:0000738,CL:0002087,CL:0000255,CL:0002031,CL:0000576,CL:0000235,CL:0000037,CL:0000566,CL:0000049,CL:0000557,CL:0000129,CL:0002453,CL:0000837,CL:0000133,CL:0002009,CL:0000339,CL:0000040,CL:0000559
+|accession_numbers=CAGE;DRX008829;DRR009701;DRZ001126;DRZ002511;DRZ012476;DRZ013861
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000479,UBERON:0004121,UBERON:0011216,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0001017,UBERON:0001016
+|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0000763,CL:0002371,CL:0000766,CL:0002319,CL:0000095,CL:0000243,CL:0000878,CL:0000219,CL:0000325,CL:0000473,CL:0000234,CL:0000125,CL:0000738,CL:0000255,CL:0000235,CL:0000864,CL:0000129
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000113
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr16:91270004..91270023,+!p1@Olig1!3.02!1182.62!Olig1;;chr11:116196664..116196679,-!p1@Foxj1!2.89!1158.80!Foxj1;;chr5:138199361..138199441,+!p2@Tsc22d4!2.48!552.51!Tsc22d4;;chr16:91225808..91225824,+!p1@Olig2!2.41!254.35!Olig2;;chr3:34548909..34548927,+!p1@Sox2!2.04!179.43!Sox2;;chr16:91270091..91270143,+!p2@Olig1!1.90!77.61!Olig1;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.80!78.38!Pou3f3;;chr17:25707623..25707639,-!p1@Sox8!1.74!219.39!Sox8;;chr3:34548946..34548972,+!p2@Sox2!1.70!54.17!Sox2;;chrX:58146612..58146615,-!p1@Sox3!1.66!44.95!Sox3;;chr7:25292141..25292158,+!p2@Zfp428!1.62!137.93!Zfp428;;chr2:38206744..38206766,+!p1@Lhx2!1.59!45.34!Lhx2;;chr13:99124189..99124205,+!p1@Foxd1!1.53!49.56!Foxd1;;chr10:84218895..84218909,+!p1@Rfx4!1.53!32.66!Rfx4;;chr8:12395603..12395621,+!p1@Sox1!1.52!32.27!Sox1;;chr10:86956396..86956411,-!p1@Ascl1!1.51!47.64!Ascl1;;chrX:90531838..90531861,+!p1@Arx!1.51!39.19!Arx;;chr13:48356475..48356492,+!p1@Id4!1.50!633.58!Id4;;chr12:54349410..54349461,+!p1@Npas3!1.48!34.58!Npas3;;chr14:122874619..122874634,+!p1@Zic2!1.45!26.90!Zic2;;chr7:52960700..52960719,+!p2@Dbp!1.44!32.27!Dbp;;chr2:90936901..90936945,+!p1@Sfpi1!1.43!131.79!Sfpi1;;chr14:118636214..118636235,-!p1@Sox21!1.42!29.97!Sox21;;chr3:34549096..34549111,+!p3@Sox2!1.42!25.36!Sox2;;chr4:135699731..135699747,+!p1@Id3!1.37!2408.28!Id3;;chr15:78994907..78994926,-!p1@Sox10!1.37!56.86!Sox10;;chr10:84218800..84218829,+!p2@Rfx4!1.36!21.90!Rfx4;;chr14:118636238..118636257,-!p2@Sox21!1.34!20.75!Sox21;;chr7:52960555..52960662,+!p1@Dbp!1.31!160.22!Dbp;;chr17:56970339..56970428,-!p1@Rfx2!1.31!60.32!Rfx2;;chr9:91260616..91260653,-!p2@Zic1!1.31!19.60!Zic1;;chr12:86814833..86814846,+!p1@Fos!1.30!431.48!Fos;;chr9:91260594..91260612,-!p1@Zic1!1.30!18.83!Zic1;;chr11:112643496..112643562,+!p1@Sox9!1.26!617.05!Sox9;;chr16:15887371..15887385,+!p1@Cebpd!1.26!572.10!Cebpd;;chr9:106356278..106356292,+!p3@Pcbp4!1.26!29.58!Pcbp4;;chr5:148000254..148000260,+!p1@Gsx1!1.25!16.91!Gsx1;;chr11:60023912..60023930,-!p1@Srebf1!1.24!388.83!Srebf1;;chr4:107353376..107353452,-!p3@Dmrtb1!1.21!15.37!Dmrtb1;;chr7:25292160..25292213,+!p3@Zfp428!1.20!36.88!Zfp428;;chr7:52960663..52960677,+!p6@Dbp!1.20!14.98!Dbp;;chr11:21901608..21901634,-!p1@Otx1!1.20!14.98!Otx1;;chr2:90936947..90936977,+!p2@Sfpi1!1.19!28.43!Sfpi1;;chr14:52948124..52948148,-!p7@Sall2!1.18!14.22!Sall2;;chr6:145813905..145813932,-!p2@Bhlhe41!1.16!25.36!Bhlhe41;;chr4:154010409..154010466,-!p2@Prdm16!1.15!30.35!Prdm16;;chr8:87225329..87225396,+!p1@Lyl1!1.14!48.41!Lyl1;;chr5:38215819..38215823,-!p1@Msx1!1.14!33.43!Msx1;;chrX:108009761..108009788,+!p1@Pou3f4!1.14!12.68!Pou3f4;;chr2:30700881..30700916,+!p1@Prrx2!1.13!23.82!Prrx2;;chr6:145814003..145814056,-!p1@Bhlhe41!1.12!35.35!Bhlhe41;;chr8:87297280..87297326,-!p2@Nfix!1.12!28.43!Nfix;;chr13:72101161..72101177,-!p2@Irx1!1.12!16.91!Irx1;;chr2:71384802..71384815,-!p1@Dlx2!1.12!14.98!Dlx2;;chr5:138199339..138199346,+!p18@Tsc22d4!1.12!12.29!Tsc22d4;;chr5:77524250..77524300,-!p1@Hopx!1.11!240.90!Hopx;;chr16:91225654..91225671,+!p2@Olig2!1.10!11.53!Olig2;;chr13:72101178..72101203,-!p1@Irx1!1.09!17.67!Irx1;;chr3:8666997..8667012,-!p2@Hey1!1.08!25.36!Hey1;;chr7:146768691..146768707,-!p1@Nkx6-2!1.08!11.14!Nkx6-2;;chr8:87238155..87238187,-!p13@Nfix!1.04!9.99!Nfix;;chr9:106356265..106356276,+!p4@Pcbp4!1.03!16.14!Pcbp4;;chr8:12395874..12395885,+!p2@Sox1!1.03!9.61!Sox1;;chr6:29476690..29476724,+!p1@Irf5!1.02!44.95!Irf5;;chr8:94325321..94325366,-!p1@Irx3!1.02!23.44!Irx3;;chr7:52960730..52960762,+!p3@Dbp!1.01!11.91!Dbp;;chr17:86087592..86087615,-!p1@Six2!1.01!9.22!Six2;;chr7:122968213..122968266,-!p4@Sox6!1.00!10.76!Sox6;;chr3:8666963..8666978,-!p1@Hey1!0.99!58.40!Hey1;;chr11:98636531..98636559,-!p1@Nr1d1!0.99!50.72!Nr1d1;;chr8:87297878..87297935,-!p3@Nfix!0.99!19.60!Nfix;;chr13:53568104..53568156,-!p1@Msx2!0.99!13.06!Msx2;;chr5:138199481..138199491,+!p16@Tsc22d4!0.98!8.45!Tsc22d4;;chr2:147012125..147012149,-!p1@Nkx2-2!0.98!8.45!Nkx2-2;;chr10:42303385..42303401,-!p1@Nr2e1!0.98!8.45!Nr2e1;;chr3:34549144..34549155,+!p5@Sox2!0.98!8.45!Sox2;;chr11:5761979..5761992,+!p2@Aebp1!0.97!17.29!Aebp1;;chr2:30700857..30700873,+!p3@Prrx2!0.97!11.53!Prrx2;;chr2:152561980..152561997,+!p1@Id1!0.96!243.59!Id1;;chr15:103170516..103170531,-!p2@Zfp385a!0.96!19.60!Zfp385a;;chr2:90936978..90937023,+!p3@Sfpi1!0.96!15.75!Sfpi1;;chr4:154335024..154335039,+!p1@Hes5!0.96!9.99!Hes5;;chr13:31898767..31898785,+!p4@Foxc1!0.96!9.99!Foxc1;;chr16:91269972..91269978,+!p3@Olig1!0.96!8.07!Olig1;;chr1:193007123..193007139,-!p1@Atf3!0.95!45.34!Atf3;;chr11:5761889..5761969,+!p1@Aebp1!0.94!333.89!Aebp1;;chr8:87502608..87502623,-!p1@Junb!0.94!130.63!Junb;;chr2:127347067..127347093,-!p1@Kcnip3!0.94!13.06!Kcnip3;;chr4:99322820..99322845,+!p1@Foxd3!0.94!9.99!Foxd3;;chr4:107353455..107353476,-!p8@Dmrtb1!0.94!7.68!Dmrtb1;;chr1:78193687..78193692,-!p1@Pax3!0.94!7.68!Pax3;;chr8:28087609..28087634,+!p1@Zfp703!0.93!178.28!Zfp703;;chr8:72356532..72356611,+!p1@Pbx4!0.92!31.12!Pbx4;;chr5:77524231..77524245,-!p3@Hopx!0.92!18.83!Hopx;;chr1:91827756..91827773,-!p1@Gbx2!0.92!7.30!Gbx2;;chr4:107353346..107353375,-!p5@Dmrtb1!0.92!7.30!Dmrtb1;;chr4:109650609..109650653,+!p1@Dmrta2!0.92!7.30!Dmrta2;;chrX:55283799..55283813,+!p1@Zic3!0.92!7.30!Zic3;;chr14:122874593..122874610,+!p2@Zic2!0.92!7.30!Zic2;;chr14:118635860..118635885,-!p3@Sox21!0.92!7.30!Sox21;;chr7:25292331..25292421,+!p1@Zfp428!0.91!52.64!Zfp428;;chr6:72185232..72185272,-!p1@Atoh8!0.91!21.13!Atoh8;;chrX:7341077..7341091,+!p5@Tfe3!0.91!12.29!Tfe3;;chr19:5423800..5423821,-!p5@Drap1!0.91!10.76!Drap1;;chr15:103164702..103164778,-!p3@Zfp385a!0.91!8.45!Zfp385a;;chr13:40829137..40829205,-!p1@Tfap2a!0.91!8.07!Tfap2a;;chr7:35904304..35904320,+!p1@Cebpa!0.90!147.16!Cebpa;;chr7:52960888..52960902,+!p7@Dbp!0.90!6.92!Dbp;;chr2:147019977..147019985,-!p2@Nkx2-2!0.90!6.92!Nkx2-2;;chr18:35020854..35020869,+!p1@Egr1!0.89!270.87!Egr1;;chr12:34642510..34642530,+!p1@Twist1!0.89!22.28!Twist1;;chr6:47998938..47998955,-!p2@Zfp777!0.89!9.22!Zfp777;;chr19:59533221..59533271,+!p1@Emx2!0.89!8.45!Emx2;;chr6:47998855..47998863,-!p5@Zfp777!0.89!7.68!Zfp777;;chr8:94881872..94881887,+!p2@Irx5!0.89!7.30!Irx5;;chr8:123260252..123260264,+!p1@Irf8!0.88!48.41!Irf8;;chr14:52634234..52634281,-!p3@Zfp219!0.88!19.21!Zfp219;;chr13:72766279..72766296,+!p2@Irx2!0.88!9.99!Irx2;;chr13:78339428..78339466,-!p2@Nr2f1!0.88!9.22!Nr2f1;;chr13:78338076..78338104,-!p4@Nr2f1!0.88!8.45!Nr2f1;;chr15:95485240..95485257,-!p1@Dbx2!0.88!6.53!Dbx2;;chr11:116196714..116196729,-!p2@Foxj1!0.88!6.53!Foxj1;;chr9:106356243..106356264,+!p2@Pcbp4!0.87!29.58!Pcbp4;;chr2:30700788..30700824,+!p2@Prrx2!0.87!9.99!Prrx2;;chr2:160192793..160192809,-!p1@Mafb!0.86!99.51!Mafb;;chr11:98603160..98603171,+!p3@Thra!0.86!30.74!Thra;;chr19:19185671..19185693,-!p1@Rorb!0.85!15.37!Rorb;;chr13:31898637..31898653,+!p2@Foxc1!0.85!11.14!Foxc1;;chr13:72101141..72101158,-!p3@Irx1!0.85!7.68!Irx1;;chr8:12395892..12395919,+!p4@Sox1!0.85!6.15!Sox1;;chr8:87324243..87324277,-!p1@Nfix!0.84!152.92!Nfix;;chr8:123640063..123640077,+!p1@Foxc2!0.84!11.14!Foxc2;;chr3:8667033..8667046,-!p3@Hey1!0.84!8.45!Hey1;;chr19:55816546..55816556,+!p3@Tcf7l2!0.83!23.05!Tcf7l2;;chr17:86020115..86020128,+!p2@Six3!0.83!5.76!Six3;;chr3:34548845..34548856,+!p4@Sox2!0.83!5.76!Sox2;;chr14:122874718..122874729,+!p3@Zic2!0.83!5.76!Zic2;;chr9:106356211..106356242,+!p1@Pcbp4!0.82!116.42!Pcbp4;;chr17:34784132..34784161,+!p1@Atf6b!0.82!34.58!Atf6b;;chr16:43363190..43363242,+!p2@Zbtb20!0.82!18.44!Zbtb20;;chr7:91558392..91558434,-!p1@Arnt2!0.82!16.52!Arnt2;;chr6:72185210..72185228,-!p3@Atoh8!0.82!9.99!Atoh8;;chr7:25292076..25292114,+!p4@Zfp428!0.81!15.75!Zfp428;;chr10:80870405..80870428,-!p4@Nfic!0.80!15.37!Nfic;;chr13:31898729..31898761,+!p1@Foxc1!0.80!13.83!Foxc1;;chr13:72766250..72766273,+!p1@Irx2!0.80!8.45!Irx2;;chr6:145813964..145813994,-!p3@Bhlhe41!0.80!6.92!Bhlhe41;;chr5:28492230..28492257,+!p1@En2!0.80!5.38!En2;;chr8:86590801..86590818,+!p2@Rfx1!0.80!5.38!Rfx1;;chr3:107398056..107398082,+!p1@Alx3!0.80!5.38!Alx3;;chr4:22415443..22415506,-!p1@Pou3f2!0.80!5.38!Pou3f2;;chr15:81977802..81977828,+!p2@Srebf2!0.79!48.41!Srebf2;;chr15:103170533..103170556,-!p1@Zfp385a!0.78!20.36!Zfp385a;;chr7:134169648..134169657,-!p14@Maz!0.78!7.30!Maz;;chr8:87298020..87298041,-!p9@Nfix!0.78!4.99!Nfix;;chr6:72185553..72185612,-!p2@Atoh8!0.76!9.61!Atoh8;;chr13:78339476..78339515,-!p1@Nr2f1!0.76!7.68!Nr2f1;;chr13:78339382..78339420,-!p3@Nr2f1!0.76!5.76!Nr2f1;;chr7:52071956..52071978,-!p1@Atf5!0.75!166.75!Atf5;;chr11:96690797..96690813,-!p1@Nfe2l1!0.75!98.36!Nfe2l1;;chr19:5424822..5424845,-!p3@Drap1!0.75!19.98!Drap1;;chr5:138188113..138188145,+!p9@Tsc22d4!0.75!7.68!Tsc22d4;;chr2:71367871..71367898,+!p1@Dlx1!0.75!4.61!Dlx1;;chr1:186556410..186556424,-!p1@Hlx!0.74!15.37!Hlx;;chr2:173044380..173044432,-!p1@Zbp1!0.74!11.53!Zbp1;;chr13:31898496..31898519,+!p3@Foxc1!0.74!7.68!Foxc1;;chr13:78339134..78339185,-!p5@Nr2f1!0.74!5.76!Nr2f1;;chr8:94325273..94325288,-!p5@Irx3!0.74!5.76!Irx3;;chr8:87324171..87324182,-!p6@Nfix!0.73!8.07!Nfix;;chr11:98603185..98603208,+!p1@Thra!0.72!288.16!Thra;;chrX:7339938..7339963,+!p1@Tfe3!0.72!24.21!Tfe3;;chr7:30088977..30089002,+!p2@Dpf1!0.72!6.15!Dpf1;;chr8:87297330..87297365,-!p5@Nfix!0.72!4.23!Nfix;;chr15:95485210..95485225,-!p2@Dbx2!0.72!4.23!Dbx2;;chr1:91827728..91827743,-!p2@Gbx2!0.72!4.23!Gbx2;;chr3:96001503..96001557,-!p1@Bola1!0.71!99.90!Bola1;;chr19:5424768..5424811,-!p2@Drap1!0.71!89.52!Drap1;;chr2:167514456..167514473,+!p1@Cebpb!0.70!205.17!Cebpb;;chr11:98603119..98603130,+!p2@Thra!0.70!38.42!Thra;;chr19:28754692..28754757,-!p1@Glis3!0.70!18.83!Glis3;;chr11:98605517..98605539,+!p5@Thra!0.70!6.15!Thra;;chr16:92697560..92697592,-!p2@Runx1!0.69!28.05!Runx1;;chr15:81977766..81977789,+!p3@Srebf2!0.69!27.28!Srebf2;;chr7:5003165..5003203,+!p2@Zfp580!0.69!24.59!Zfp580;;chr7:87170879..87170914,+!p2@Zfp710!0.69!9.99!Zfp710;;chr6:90412608..90412630,+!p2@Klf15!0.69!8.84!Klf15;;chr2:71384458..71384526,-!p2@Dlx2!0.69!3.84!Dlx2;;chr10:84218931..84218942,+!p4@Rfx4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+|ffid_belonging_in_development=CL:0000133,CL:0000049,CL:0000134,CL:0000339,CL:0000221
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 36: / Line 42: @@
 |has_quality=
 |id=FF:11736-123E8
-|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0000113
+|is_a=EFO:0002091;;FF:0000113
+|is_obsolete=
+|library_id=CNhs12634
+|library_id_phase_based=2:CNhs12634
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11736
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11736
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Microglia%252c%2520donor2.CNhs12634.11736-123E8.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Microglia%252c%2520donor2.CNhs12634.11736-123E8.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Microglia%252c%2520donor2.CNhs12634.11736-123E8.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Microglia%252c%2520donor2.CNhs12634.11736-123E8.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Microglia%252c%2520donor2.CNhs12634.11736-123E8.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Microglia, donor2
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12634,LSID952,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.11779559634038,0,0,0,0,0,-0.487855059711492,0,0,0,0,-0.0843392403965415,0,0,0,0,0.123794748603148,0,-0.191893350882575,0,0,0,0,0,0,0,0,0,0,0,0,0.290281956245014,-0.558422792324031,0,0,0,0,0,-0.0855279768926776,0.141204588184303,-0.126321555190113,-0.464999191010043,-0.269868638010351,0.404298764158439,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,-0.0428469550828748,0,0.0357906421910787,0,0,0,-0.243225778194271,-0.310650657339386,-0.158091042771083,-0.140687683267293,0,-0.0780086007519514,0.0258086638965003,0.0806141946632426,0,0,0,0.0516176905055615,0.70133548796799,-0.0788315948399074,0,0,0,0,0,0,0.404040132573604,0.436963650017243,0.448399755839744,0,0,0,0.34267782519752,0
 |rna_box=123
 |rna_catalog_number=custom
@@ Line 54: / Line 73: @@
 |rna_rin=
 |rna_sample_type=total RNA
-|rna_tube_id=123E8
+|rna_tube_id=1.23E+10
 |rna_weight_ug=10
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 76: / Line 96: @@
 |sample_tissue=brain
 |top_motifs=ZNF423:3.45005045587;GTF2A1,2:3.35580476845;EBF1:3.23772402366;TFAP2{A,C}:2.52171136418;RFX1:2.27406682305;TFCP2:2.27229481451;ESR1:2.26462131523;HMX1:2.2046794543;HES1:2.05396489308;ZIC1..3:1.89596361568;TP53:1.80457456429;TFAP4:1.73960427643;NR1H4:1.73615239877;MTF1:1.69519893147;RXR{A,B,G}:1.65946055349;EP300:1.64789723742;HAND1,2:1.60120595501;ZNF148:1.53847056328;ZBTB6:1.48310391722;BACH2:1.36274350375;RFX2..5_RFXANK_RFXAP:1.33596546819;POU2F1..3:1.32194067009;UFEwm:1.27284227081;PATZ1:1.2405365896;TLX1..3_NFIC{dimer}:1.20628659986;PAX5:1.17012309051;MYOD1:1.15695270894;NFE2L1:1.13175693606;RREB1:1.11080599922;MTE{core}:1.08333873098;GLI1..3:1.06433064083;TFAP2B:1.01583236086;IKZF1:1.00416210916;SP1:0.975400810093;HOXA9_MEIS1:0.968016181847;HIC1:0.955720335694;RXRA_VDR{dimer}:0.913887987243;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.884634581826;MAZ:0.881980465262;SMAD1..7,9:0.850167768834;REST:0.798871190023;FOXM1:0.786800092277;GTF2I:0.774316661349;ATF6:0.760886620488;POU5F1:0.726957435225;LMO2:0.703524818497;KLF4:0.686353925619;FOXO1,3,4:0.678310741858;VSX1,2:0.667128505023;XCPE1{core}:0.631906816415;TEAD1:0.628560612839;MED-1{core}:0.612204300908;NHLH1,2:0.579794763895;GCM1,2:0.57826768965;RUNX1..3:0.469448429323;GATA4:0.468101780297;HOX{A5,B5}:0.461179557057;SOX2:0.446294567695;SPIB:0.442797485771;MZF1:0.432683262308;FOS_FOS{B,L1}_JUN{B,D}:0.401323748042;NKX3-2:0.399683158877;FOXN1:0.389094707394;EGR1..3:0.388544619865;STAT2,4,6:0.387712529081;TOPORS:0.382170896371;TBX4,5:0.358058330678;SPZ1:0.347377753834;ZNF384:0.344560469254;ZFP161:0.31991980923;ATF4:0.318942328072;TFDP1:0.294511004969;NFE2L2:0.291620260245;NFIL3:0.267078089668;MYFfamily:0.266601935529;OCT4_SOX2{dimer}:0.257670408666;PRDM1:0.232061596259;NR5A1,2:0.199369030263;HIF1A:0.179670773385;FOX{F1,F2,J1}:0.177526842617;PAX1,9:0.176373818928;BREu{core}:0.156371057354;JUN:0.131333082525;ZNF238:0.122560967904;FOXP3:0.11493817222;MYBL2:0.0759503789398;NFKB1_REL_RELA:0.0579060935796;FOXL1:-0.03190014359;SPI1:-0.0527332856699;AR:-0.116041383833;IRF7:-0.138100048148;NR6A1:-0.141438690242;HBP1_HMGB_SSRP1_UBTF:-0.160854213368;LEF1_TCF7_TCF7L1,2:-0.180897564583;SOX5:-0.198981215665;HLF:-0.200126173553;NANOG{mouse}:-0.205083547036;RORA:-0.206930085559;TBP:-0.229402442241;NKX2-2,8:-0.25975200435;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.260592513257;SOX17:-0.267032040198;POU3F1..4:-0.267371158343;IRF1,2:-0.271243749685;HSF1,2:-0.276140875938;FOSL2:-0.287992044254;GFI1:-0.33405795384;MYB:-0.341466456814;ETS1,2:-0.344977894848;HNF4A_NR2F1,2:-0.373850748452;SRF:-0.373953676507;RBPJ:-0.377125565404;POU6F1:-0.379773989012;HOX{A4,D4}:-0.389792913086;ESRRA:-0.391136314142;ALX4:-0.393496631257;NFY{A,B,C}:-0.414997735667;NKX3-1:-0.430385385133;SREBF1,2:-0.455615691219;EN1,2:-0.470957985285;GZF1:-0.485274261545;ADNP_IRX_SIX_ZHX:-0.490691622598;SOX{8,9,10}:-0.50167098639;ONECUT1,2:-0.504516300559;CDC5L:-0.508586575056;PAX6:-0.527285653931;ZEB1:-0.529726360936;ARID5B:-0.540053656035;MEF2{A,B,C,D}:-0.573152420724;ATF2:-0.5837980028;PAX2:-0.585978933792;MAFB:-0.593120304628;NR3C1:-0.594819008473;FOX{D1,D2}:-0.598779915097;DMAP1_NCOR{1,2}_SMARC:-0.602162302018;HMGA1,2:-0.608929372586;TAL1_TCF{3,4,12}:-0.640175197482;PAX4:-0.641584854956;ZNF143:-0.657669361767;HNF1A:-0.699250953611;PAX8:-0.701111586314;STAT1,3:-0.709920586014;DBP:-0.711153654175;NANOG:-0.723886770214;STAT5{A,B}:-0.735365788104;CREB1:-0.752677331938;TLX2:-0.759329073983;GFI1B:-0.770253713078;NKX2-3_NKX2-5:-0.787486671337;SNAI1..3:-0.792248229282;PPARG:-0.854715403914;IKZF2:-0.869920568862;LHX3,4:-0.879956195167;NRF1:-0.901710404141;ELK1,4_GABP{A,B1}:-0.903477812884;CUX2:-0.917905369501;CRX:-0.917912036557;PBX1:-0.948402483908;CEBPA,B_DDIT3:-0.991954578246;ALX1:-0.998087868878;ELF1,2,4:-1.05830639132;PRRX1,2:-1.13244590164;NFE2:-1.15784180504;NFATC1..3:-1.1592564503;T:-1.19881493989;E2F1..5:-1.20072598172;BPTF:-1.20697312809;ZBTB16:-1.23076615696;ATF5_CREB3:-1.24659361091;GATA6:-1.30847056115;bHLH_family:-1.36280650333;AHR_ARNT_ARNT2:-1.40008652395;NFIX:-1.4073662254;NKX2-1,4:-1.41613167451;YY1:-1.44102090382;NKX6-1,2:-1.56789526174;TGIF1:-1.57301088846;PITX1..3:-1.59470631149;FOXA2:-1.66809055955;FOX{I1,J2}:-1.70980180945;EVI1:-1.81158765122;POU1F1:-1.81275209114;PDX1:-1.81906902842;FOXP1:-1.83986204308;FOXQ1:-1.96360515583;TEF:-2.01500127769;FOXD3:-2.11184933752;CDX1,2,4:-2.74663059449;AIRE:-2.82541848388
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11736-123E8;search_select_hide=table117:11736-123E8
 }}

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FF:11736-123E8: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:16, 4 June 2020

CNhs12634

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	Mozilla Cavendish skin modified by DaSch for the Web Community Wiki GitHub project page – Report a bug – Skin version: 2.6.0