FF:16-22A4: Difference between revisions

Latest revision as of 19:08, 4 June 2020

Name:	corpora quadrigemina, adult
Species:	Mouse (Mus musculus)
Library ID:	CNhs10501
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	corpora quadrigemina
dev stage	adult
sex	male
age	NA
cell type	CELL MIXTURE - tissue sample
cell line	NA
company	NA
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	NA
catalog number	NA
sample type	NA
extraction protocol (Details)	NA

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005905

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10501		CAGE		DRX008944		DRR009818

Accession ID Mm9

Library id		BAM		CTSS
CNhs10501		DRZ001243		DRZ002626

Accession ID Mm10

Library id		BAM		CTSS
CNhs10501		DRZ012593		DRZ013976

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

CNhs10501

0	0
1	0.774
10	0
100	0
1000	0
1001	0.0707
1002	-0.0795
1003	0.0715
1004	0
1005	0
1006	0.677
1007	-0.0857
1008	0
1009	-0.0572
101	-0.0525
1010	0
1011	0.477
1012	0.204
1013	0.249
1014	-0.0245
1015	-0.0749
1016	-0.127
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	0.0775
1023	0
1024	0.103
1025	0
1026	0
1027	0.375
1028	0
1029	0.0464
103	-0.0861
1030	0
1031	-0.327
1032	0.43
1033	-0.0665
1034	0
1035	0
1036	-0.179
1037	0
1038	-0.188
1039	0.219
104	0
1040	-0.181
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: CNhs10501

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0015
MA0003.1	MA0003.1	0.321
MA0004.1	MA0004.1	0.509
MA0006.1	MA0006.1	0.182
MA0007.1	MA0007.1	0.334
MA0009.1	MA0009.1	0.843
MA0014.1	MA0014.1	0.747
MA0017.1	MA0017.1	3.45883e-6
MA0018.2	MA0018.2	0.0155
MA0019.1	MA0019.1	0.527
MA0024.1	MA0024.1	0.0613
MA0025.1	MA0025.1	5.69827e-4
MA0027.1	MA0027.1	0.0785
MA0028.1	MA0028.1	0.112
MA0029.1	MA0029.1	0.899
MA0030.1	MA0030.1	0.937
MA0031.1	MA0031.1	0.254
MA0035.2	MA0035.2	0.0286
MA0038.1	MA0038.1	0.393
MA0039.2	MA0039.2	0.0254
MA0040.1	MA0040.1	0.377
MA0041.1	MA0041.1	0.0691
MA0042.1	MA0042.1	0.209
MA0043.1	MA0043.1	0.028
MA0046.1	MA0046.1	4.26383e-11
MA0047.2	MA0047.2	2.02389e-4
MA0048.1	MA0048.1	0.032
MA0050.1	MA0050.1	9.55222e-5
MA0051.1	MA0051.1	0.00102
MA0052.1	MA0052.1	0.493
MA0055.1	MA0055.1	0.0083
MA0057.1	MA0057.1	0.349
MA0058.1	MA0058.1	0.501
MA0059.1	MA0059.1	0.152
MA0060.1	MA0060.1	0.931
MA0061.1	MA0061.1	0.0281
MA0062.2	MA0062.2	0.00287
MA0065.2	MA0065.2	2.47898e-6
MA0066.1	MA0066.1	0.0361
MA0067.1	MA0067.1	0.442
MA0068.1	MA0068.1	0.336
MA0069.1	MA0069.1	0.0648
MA0070.1	MA0070.1	0.339
MA0071.1	MA0071.1	0.168
MA0072.1	MA0072.1	0.699
MA0073.1	MA0073.1	0.797
MA0074.1	MA0074.1	0.134
MA0076.1	MA0076.1	0.277
MA0077.1	MA0077.1	0.425
MA0078.1	MA0078.1	0.803
MA0079.2	MA0079.2	0.405
MA0080.2	MA0080.2	8.66167e-10
MA0081.1	MA0081.1	0.231
MA0083.1	MA0083.1	0.00407
MA0084.1	MA0084.1	0.674
MA0087.1	MA0087.1	0.0976
MA0088.1	MA0088.1	0.375
MA0090.1	MA0090.1	0.123
MA0091.1	MA0091.1	0.0926
MA0092.1	MA0092.1	0.159
MA0093.1	MA0093.1	0.58
MA0099.2	MA0099.2	0.00129
MA0100.1	MA0100.1	0.278
MA0101.1	MA0101.1	0.0136
MA0102.2	MA0102.2	0.556
MA0103.1	MA0103.1	0.179
MA0104.2	MA0104.2	0.844
MA0105.1	MA0105.1	0.00674
MA0106.1	MA0106.1	0.0548
MA0107.1	MA0107.1	0.03
MA0108.2	MA0108.2	2.4474e-4
MA0111.1	MA0111.1	0.895
MA0112.2	MA0112.2	0.00109
MA0113.1	MA0113.1	0.363
MA0114.1	MA0114.1	1.09435e-5
MA0115.1	MA0115.1	3.14388e-5
MA0116.1	MA0116.1	0.0669
MA0117.1	MA0117.1	0.964
MA0119.1	MA0119.1	0.13
MA0122.1	MA0122.1	0.959
MA0124.1	MA0124.1	0.509
MA0125.1	MA0125.1	0.0364
MA0131.1	MA0131.1	0.742
MA0135.1	MA0135.1	0.315
MA0136.1	MA0136.1	9.90414e-12
MA0137.2	MA0137.2	0.314
MA0138.2	MA0138.2	9.05945e-5
MA0139.1	MA0139.1	0.601
MA0140.1	MA0140.1	7.76019e-5
MA0141.1	MA0141.1	0.0122
MA0142.1	MA0142.1	0.138
MA0143.1	MA0143.1	0.623
MA0144.1	MA0144.1	0.0859
MA0145.1	MA0145.1	0.144
MA0146.1	MA0146.1	0.0377
MA0147.1	MA0147.1	0.682
MA0148.1	MA0148.1	6.90018e-4
MA0149.1	MA0149.1	0.158
MA0150.1	MA0150.1	0.156
MA0152.1	MA0152.1	0.246
MA0153.1	MA0153.1	5.98758e-12
MA0154.1	MA0154.1	0.0321
MA0155.1	MA0155.1	0.412
MA0156.1	MA0156.1	1.36334e-7
MA0157.1	MA0157.1	0.176
MA0159.1	MA0159.1	0.00323
MA0160.1	MA0160.1	0.0151
MA0162.1	MA0162.1	0.238
MA0163.1	MA0163.1	9.61734e-4
MA0164.1	MA0164.1	0.882
MA0258.1	MA0258.1	0.0184
MA0259.1	MA0259.1	0.829

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: CNhs10501

Novel motif	Logo	P-value
1	1	0.234
10	10	0.0523
100	100	0.38
101	101	0.827
102	102	0.933
103	103	0.104
104	104	0.962
105	105	0.581
106	106	0.029
107	107	0.109
108	108	0.611
109	109	0.0134
11	11	0.0918
110	110	0.0472
111	111	0.281
112	112	0.0155
113	113	0.507
114	114	0.516
115	115	0.686
116	116	0.175
117	117	0.00413
118	118	0.339
119	119	0.237
12	12	0.846
120	120	1
121	121	0.673
122	122	0.61
123	123	3.04315e-4
124	124	0.0427
125	125	0.154
126	126	0.0208
127	127	0.244
128	128	0.0408
129	129	0.318
13	13	1.74881e-7
130	130	0.136
131	131	0.421
132	132	0.671
133	133	0.745
134	134	0.112
135	135	0.13
136	136	0.0559
137	137	0.703
138	138	0.969
139	139	0.216
14	14	0.766
140	140	0.022
141	141	0.972
142	142	0.531
143	143	0.251
144	144	0.734
145	145	2.06086e-4
146	146	0.3
147	147	0.351
148	148	0.723
149	149	0.924
15	15	0.198
150	150	0.0702
151	151	0.873
152	152	0.0926
153	153	0.781
154	154	0.726
155	155	0.463
156	156	0.00522
157	157	0.254
158	158	0.389
159	159	0.546
160	160	0.213
161	161	0.166
162	162	0.696
163	163	0.565
164	164	0.0451
165	165	0.175
166	166	0.684
167	167	0.729
168	168	0.648
169	169	0.00435
17	17	0.0478
18	18	0.97
19	19	0.136
2	2	0.718
20	20	0.0239
21	21	0.158
22	22	0.174
23	23	0.667
24	24	0.057
25	25	0.771
26	26	3.87928e-9
27	27	0.399
28	28	0.752
29	29	0.0396
3	3	0.0957
30	30	0.845
31	31	0.75
32	32	0.622
33	33	0.168
34	34	0.781
35	35	0.783
36	36	0.269
37	37	0.0316
38	38	0.528
39	39	0.314
4	4	0.237
40	40	0.104
41	41	0.407
42	42	0.228
43	43	0.139
44	44	0.369
45	45	0.73
46	46	0.0509
47	47	0.477
48	48	0.337
49	49	0.198
5	5	0.189
50	50	0.264
51	51	0.82
52	52	0.28
53	53	0.402
54	54	0.945
55	55	0.947
56	56	0.499
57	57	0.515
58	58	0.365
59	59	0.111
6	6	0.945
60	60	0.0333
61	61	0.0671
62	62	0.237
63	63	0.164
64	64	0.654
65	65	0.406
66	66	0.871
67	67	0.785
68	68	0.891
69	69	0.514
7	7	0.0193
70	70	0.106
71	71	0.00219
72	72	0.616
73	73	0.039
74	74	0.871
75	75	0.0552
76	76	0.374
77	77	0.357
78	78	0.00224
79	79	0.411
8	8	0.0618
80	80	0.747
81	81	0.769
82	82	0.349
83	83	0.145
84	84	0.848
85	85	0.24
86	86	0.136
87	87	0.178
88	88	0.475
89	89	0.729
9	9	0.49
90	90	0.148
91	91	0.0432
92	92	0.34
93	93	0.0853
94	94	0.773
95	95	0.0434
96	96	0.496
97	97	0.962
98	98	0.708
99	99	0.521

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: CNhs10501

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011283 mouse corpora quadrigemina- adult 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

UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
0000955 (brain)
0002259 (corpora quadrigemina)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002950 (regional part of midbrain)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001891 (midbrain)
0002314 (midbrain tectum)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011283 (mouse corpora quadrigemina- adult 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
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0006777 (tectal plate)
UBERON:0010316 (germ layer / neural crest)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000922,UBERON:0000955,UBERON:0000483,UBERON:0002259,UBERON:0000033,UBERON:0000479,UBERON:0002346,UBERON:0000064,UBERON:0000073,UBERON:0004121,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0000025,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0000477,UBERON:0000467,UBERON:0002616,UBERON:0001062,UBERON:0000119,UBERON:0005291,UBERON:0002950,UBERON:0006598,UBERON:0002532,UBERON:0001017,UBERON:0001016,UBERON:0000153,UBERON:0007811,UBERON:0000924,UBERON:0005743,UBERON:0002298,UBERON:0001891,UBERON:0002314,UBERON:0003075,UBERON:0003056,UBERON:0001049,UBERON:0006238,UBERON:0006601,UBERON:0005068,UBERON:0006241,UBERON:0003080,UBERON:0009616,UBERON:0006777,UBERON:0005882,UBERON:0007284,UBERON:0007135
+|DRA_sample_Accession=CAGE@SAMD00005905
+|accession_numbers=CAGE;DRX008944;DRR009818;DRZ001243;DRZ002626;DRZ012593;DRZ013976
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000955,UBERON:0002259,UBERON:0000479,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002616,UBERON:0002950,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001891,UBERON:0002314
 |ancestors_in_cell_lineage_facet=
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000998,FF:0000004,FF:0011283
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr16:91270004..91270023,+!p1@Olig1!2.26!204.46!Olig1;;chr5:138199361..138199441,+!p2@Tsc22d4!1.99!175.55!Tsc22d4;;chr17:48015839..48015915,-!p3@Foxp4!1.72!60.22!Foxp4;;chr12:30219426..30219506,+!p2@Myt1l!1.69!48.53!Myt1l;;chr16:91225808..91225824,+!p1@Olig2!1.66!45.24!Olig2;;chr2:163051181..163051205,+!p2@Tox2!1.66!44.79!Tox2;;chr7:116154364..116154444,+!p1@Tub!1.64!72.50!Tub;;chrX:34442872..34442899,-!p1@Nkrf!1.56!44.94!Nkrf;;chr4:58956447..58956510,+!p1@Zkscan16!1.53!70.55!Zkscan16;;chr2:65683890..65683907,+!p1@Csrnp3!1.53!62.01!Csrnp3;;chr15:76353005..76353021,-!p2@Scrt1!1.52!32.35!Scrt1;;chr19:19185671..19185693,-!p1@Rorb!1.49!69.95!Rorb;;chr18:36441119..36441158,+!p2@Pura!1.46!65.76!Pura;;chr10:67375146..67375208,-!p2@Zfp365!1.45!40.59!Zfp365;;chr15:76352434..76352488,-!p4@Scrt1!1.43!25.91!Scrt1;;chr4:150482563..150482655,-!p2@Camta1!1.42!87.78!Camta1;;chr1:140739014..140739032,-!p1@Lhx9!1.42!31.61!Lhx9;;chr19:55972441..55972456,+!p18@Tcf7l2!1.41!24.42!Tcf7l2;;chr7:148008023..148008092,-!p1@Zfp941!1.40!57.07!Zfp941;;chr14:49287186..49287225,-!p1@Otx2!1.40!24.27!Otx2;;chr2:127347067..127347093,-!p1@Kcnip3!1.39!38.95!Kcnip3;;chr8:24780125..24780143,+!p1@Zmat4!1.37!31.91!Zmat4;;chr15:76352677..76352737,-!p3@Scrt1!1.34!21.12!Scrt1;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.33!25.91!Pou3f3;;chr4:150513630..150513686,-!p4@Camta1!1.33!23.22!Camta1;;chr3:95032091..95032183,-!p1@Mllt11!1.32!166.57!Mllt11;;chr17:25707623..25707639,-!p1@Sox8!1.31!81.34!Sox8;;chr2:168427068..168427115,-!p3@Nfatc2!1.30!19.02!Nfatc2;;chr7:146768691..146768707,-!p1@Nkx6-2!1.29!18.72!Nkx6-2;;chr10:67375368..67375433,-!p1@Zfp365!1.28!31.61!Zfp365;;chr8:107793688..107793736,+!p1@Hsf4!1.28!23.52!Hsf4;;chr19:55972403..55972421,+!p22@Tcf7l2!1.27!17.53!Tcf7l2;;chr12:54349410..54349461,+!p1@Npas3!1.26!20.82!Npas3;;chr15:78994907..78994926,-!p1@Sox10!1.23!40.44!Sox10;;chr9:99776566..99776612,-!p1@Sox14!1.23!16.18!Sox14;;chr1:6477388..6477419,+!p3@St18!1.21!15.28!St18;;chr2:163030219..163030258,+!p5@Tox2!1.20!14.83!Tox2;;chr10:84218800..84218829,+!p2@Rfx4!1.20!14.83!Rfx4;;chrX:108009761..108009788,+!p1@Pou3f4!1.19!14.53!Pou3f4;;chr2:127347042..127347058,-!p3@Kcnip3!1.17!13.63!Kcnip3;;chr16:91270091..91270143,+!p2@Olig1!1.15!13.18!Olig1;;chrX:34442842..34442866,-!p3@Nkrf!1.15!13.03!Nkrf;;chr13:72766250..72766273,+!p1@Irx2!1.13!19.32!Irx2;;chr19:55969923..55969944,+!p6@Tcf7l2!1.13!12.58!Tcf7l2;;chr2:163030186..163030204,+!p4@Tox2!1.13!12.43!Tox2;;chr11:90252223..90252240,-!p1@Hlf!1.12!100.66!Hlf;;chr15:103170533..103170556,-!p1@Zfp385a!1.12!45.54!Zfp385a;;chr14:104867201..104867258,-!p1@Pou4f1!1.10!16.33!Pou4f1;;chr5:122499831..122499891,-!p1@Cux2!1.09!17.38!Cux2;;chr2:162769220..162769252,+!p1@L3mbtl1!1.08!10.93!L3mbtl1;;chr11:96685444..96685473,-!p5@Nfe2l1!1.07!10.64!Nfe2l1;;chr10:84218895..84218909,+!p1@Rfx4!1.07!10.64!Rfx4;;chr3:95032515..95032553,-!p5@Mllt11!1.05!12.28!Mllt11;;chr19:55968967..55968991,+!p7@Tcf7l2!1.05!10.19!Tcf7l2;;chr9:91260616..91260653,-!p2@Zic1!1.04!10.04!Zic1;;chr11:98636531..98636559,-!p1@Nr1d1!1.03!55.57!Nr1d1;;chr9:91260594..91260612,-!p1@Zic1!1.03!9.74!Zic1;;chr15:103170516..103170531,-!p2@Zfp385a!1.02!22.77!Zfp385a;;chr13:44936126..44936164,+!p6@Jarid2!1.02!11.08!Jarid2;;chr8:12395603..12395621,+!p1@Sox1!1.02!9.59!Sox1;;chr3:34548946..34548972,+!p2@Sox2!1.01!10.19!Sox2;;chr12:30213247..30213333,+!p1@Myt1l!1.01!9.29!Myt1l;;chr19:55969946..55969973,+!p8@Tcf7l2!1.01!9.29!Tcf7l2;;chr2:65768174..65768247,+!p2@Csrnp3!1.01!9.14!Csrnp3;;chr4:150482353..150482386,-!p6@Camta1!1.01!9.14!Camta1;;chr3:95032213..95032226,-!p6@Mllt11!1.00!10.93!Mllt11;;chrX:137083127..137083138,-!p9@Tsc22d3!1.00!8.99!Tsc22d3;;chr6:117813087..117813121,+!p1@Zfp239!0.99!33.85!Zfp239;;chr2:77541432..77541474,-!p5@Zfp385b!0.99!8.84!Zfp385b;;chr7:91558392..91558434,-!p1@Arnt2!0.98!24.12!Arnt2;;chr12:72149325..72149343,+!p2@Arid4a!0.98!11.98!Arid4a;;chr14:122874619..122874634,+!p1@Zic2!0.97!8.24!Zic2;;chr2:163030164..163030178,+!p6@Tox2!0.97!8.24!Tox2;;chr14:19071466..19071550,-!p1@Nr1d2!0.96!57.52!Nr1d2;;chr6:145813905..145813932,-!p2@Bhlhe41!0.96!15.73!Bhlhe41;;chr1:19199236..19199258,+!p1@Tfap2b!0.96!8.09!Tfap2b;;chr5:28492230..28492257,+!p1@En2!0.95!7.94!En2;;chr16:91225654..91225671,+!p2@Olig2!0.95!7.94!Olig2;;chr11:90252071..90252093,-!p7@Hlf!0.95!7.94!Hlf;;chr14:34791937..34791977,-!p1@Zfp488!0.95!7.94!Zfp488;;chr4:22415443..22415506,-!p1@Pou3f2!0.95!7.94!Pou3f2;;chr3:34548909..34548927,+!p1@Sox2!0.94!13.33!Sox2;;chr3:95032197..95032208,-!p3@Mllt11!0.94!9.74!Mllt11;;chr15:103164702..103164778,-!p3@Zfp385a!0.94!9.14!Zfp385a;;chr2:181501710..181501742,+!p2@Myt1!0.94!7.79!Myt1;;chrX:70656436..70656464,+!p1@Zfp92!0.94!7.79!Zfp92;;chr2:127347094..127347111,-!p2@Kcnip3!0.93!12.58!Kcnip3;;chr4:154335024..154335039,+!p1@Hes5!0.93!9.14!Hes5;;chr2:151907546..151907561,+!p1@Scrt2!0.93!7.49!Scrt2;;chr2:25562263..25562314,+!p2@Bmyc!0.92!29.81!Bmyc;;chr6:145814003..145814056,-!p1@Bhlhe41!0.92!21.87!Bhlhe41;;chr11:116196664..116196679,-!p1@Foxj1!0.92!11.53!Foxj1;;chr2:28771380..28771413,-!p2@Barhl1!0.92!7.34!Barhl1;;chr3:95032558..95032641,-!p2@Mllt11!0.91!41.64!Mllt11;;chr6:134780163..134780197,+!p2@Crebl2!0.91!17.08!Crebl2;;chr8:12395892..12395919,+!p4@Sox1!0.91!7.19!Sox1;;chr2:115890294..115890334,-!p9@Meis2!0.90!9.74!Meis2;;chr11:90250944..90250982,-!p2@Hlf!0.89!11.53!Hlf;;chr7:91558472..91558512,-!p2@Arnt2!0.87!9.44!Arnt2;;chr19:19185697..19185711,-!p2@Rorb!0.87!8.24!Rorb;;chr19:10315179..10315241,-!p1@Gm98!0.86!69.35!Gm98;;chr1:140743964..140743976,-!p3@Lhx9!0.86!6.29!Lhx9;;chr7:52960555..52960662,+!p1@Dbp!0.85!54.97!Dbp;;chr15:81633165..81633188,+!p2@Tef!0.85!53.48!Tef;;chr15:103170561..103170572,-!p4@Zfp385a!0.85!9.14!Zfp385a;;chr8:87297878..87297935,-!p3@Nfix!0.84!13.63!Nfix;;chr2:181501745..181501778,+!p1@Myt1!0.84!5.99!Myt1;;chr17:86020156..86020183,+!p1@Six3!0.84!5.99!Six3;;chr3:66785181..66785199,-!p2@Shox2!0.84!5.99!Shox2;;chr4:22415290..22415307,-!p2@Pou3f2!0.84!5.99!Pou3f2;;chr19:55969687..55969714,+!p16@Tcf7l2!0.84!5.84!Tcf7l2;;chr2:65768149..65768173,+!p4@Csrnp3!0.84!5.84!Csrnp3;;chr1:140739042..140739054,-!p2@Lhx9!0.83!5.69!Lhx9;;chr11:98636575..98636607,-!p2@Nr1d1!0.82!21.72!Nr1d1;;chr4:124334894..124334899,+!p1@Pou3f1!0.82!7.49!Pou3f1;;chr17:27693525..27693538,+!p5@Hmga1!0.81!19.77!Hmga1;;chr14:52935860..52935874,-!p3@Sall2!0.81!8.24!Sall2;;chr1:19202352..19202354,+!p2@Tfap2b!0.81!5.39!Tfap2b;;chr19:26681865..26681900,+!p6@Smarca2!0.80!16.33!Smarca2;;chr8:112603658..112603674,+!p2@Zfp612!0.80!10.19!Zfp612;;chr15:95485240..95485257,-!p1@Dbx2!0.80!5.24!Dbx2;;chr17:86020510..86020589,+!p3@Six3!0.80!5.24!Six3;;chr11:90252108..90252134,-!p6@Hlf!0.80!5.24!Hlf;;chr19:55968937..55968951,+!p21@Tcf7l2!0.80!5.24!Tcf7l2;;chr2:168427120..168427138,-!p4@Nfatc2!0.80!5.24!Nfatc2;;chr7:17200307..17200370,-!p2@Grlf1!0.79!40.89!Grlf1;;chr9:68501522..68501538,+!p4@Rora!0.79!10.19!Rora;;chr10:80893711..80893784,-!p3@Nfic!0.78!28.31!Nfic;;chr7:30092993..30093076,+!p1@Dpf1!0.78!9.14!Dpf1;;chr18:36441100..36441113,+!p3@Pura!0.78!5.99!Pura;;chr2:151907338..151907360,+!p2@Scrt2!0.78!5.09!Scrt2;;chr11:84339016..84339044,-!p1@Lhx1!0.78!5.09!Lhx1;;chr11:70501419..70501483,-!p1@Camta2,p1@LOC100048818!0.77!56.17!Camta2;;chr7:38554763..38554780,-!p1@Zfp536!0.77!9.29!Zfp536;;chr19:23216132..23216157,+!p3@Klf9!0.77!7.94!Klf9;;chr19:55972767..55972779,+!p20@Tcf7l2!0.77!4.94!Tcf7l2;;chr2:81893535..81893548,+!p1@Zfp804a!0.77!4.94!Zfp804a;;chr8:79423144..79423178,+!p3@Nr3c2!0.76!6.89!Nr3c2;;chr3:101814061..101814094,+!p1@Nhlh2!0.76!4.79!Nhlh2;;chrX:55283799..55283813,+!p1@Zic3!0.76!4.79!Zic3;;chr5:125342568..125342602,+!p2@Zfp664!0.75!7.94!Zfp664;;chr13:72101178..72101203,-!p1@Irx1!0.75!7.49!Irx1;;chr8:79423672..79423727,+!p2@Nr3c2!0.75!5.99!Nr3c2;;chr14:118636238..118636257,-!p2@Sox21!0.75!4.64!Sox21;;chr11:21901608..21901634,-!p1@Otx1!0.75!4.64!Otx1;;chr19:55970060..55970071,+!p25@Tcf7l2!0.75!4.64!Tcf7l2;;chr7:130644017..130644092,-!p1@Zkscan2!0.74!9.29!Zkscan2;;chr9:106356278..106356292,+!p3@Pcbp4!0.74!8.09!Pcbp4;;chr13:72766279..72766296,+!p2@Irx2!0.74!7.04!Irx2;;chr9:20385868..20385902,+!p3@Zfp846!0.74!6.74!Zfp846;;chr6:145813964..145813994,-!p3@Bhlhe41!0.74!5.84!Bhlhe41;;chr8:12395874..12395885,+!p2@Sox1!0.74!4.49!Sox1;;chr17:86020115..86020128,+!p2@Six3!0.74!4.49!Six3;;chr15:82742573..82742620,-!p2@Tcf20!0.74!4.49!Tcf20;;chr12:30220074..30220102,+!p3@Myt1l!0.74!4.49!Myt1l;;chr13:44936077..44936096,+!p9@Jarid2!0.74!4.49!Jarid2;;chr1:122498955..122498968,+!p1@En1!0.74!4.49!En1;;chr1:189821714..189821761,+!p1@Esrrg!0.73!8.54!Esrrg;;chr15:81633139..81633152,+!p4@Tef!0.73!7.79!Tef;;chr14:118636214..118636235,-!p1@Sox21!0.73!5.39!Sox21;;chrX:137077151..137077227,-!p2@Tsc22d3!0.72!32.95!Tsc22d3;;chr3:130813200..130813252,+!p1@Lef1!0.72!21.27!Lef1;;chr3:95032184..95032195,-!p4@Mllt11!0.72!5.39!Mllt11;;chr2:65683842..65683856,+!p3@Csrnp3!0.72!4.19!Csrnp3;;chr8:112603610..112603656,+!p1@Zfp612!0.71!21.12!Zfp612;;chr4:149862477..149862553,+!p3@Rere!0.71!16.03!Rere;;chr3:54559496..54559511,+!p1@Smad9!0.71!10.04!Smad9;;chr4:13670626..13670657,+!p5@Runx1t1!0.71!6.74!Runx1t1;;chr13:72101141..72101158,-!p3@Irx1!0.71!5.39!Irx1;;chr14:52935876..52935928,-!p1@Sall2!0.70!36.85!Sall2;;chr10:30522690..30522752,-!p2@Ncoa7!0.70!27.41!Ncoa7;;chrX:66613481..66613562,+!p1@Aff2!0.70!19.47!Aff2;;chr2:38206580..38206600,+!p2@Lhx2!0.70!5.09!Lhx2;;chr2:38206744..38206766,+!p1@Lhx2!0.70!4.94!Lhx2;;chr10:67375223..67375240,-!p4@Zfp365!0.70!4.64!Zfp365;;chr11:96685487..96685512,-!p7@Nfe2l1!0.70!4.04!Nfe2l1;;chr3:66785201..66785226,-!p3@Shox2!0.70!4.04!Shox2;;chr9:96632719..96632745,-!p7@Zbtb38!0.70!4.04!Zbtb38;;chr3:5218516..5218544,+!p2@Zfhx4!0.69!6.14!Zfhx4;;chr19:23215554..23215567,+!p5@Klf9!0.69!5.54!Klf9;;chr11:90251852..90251855,-!p4@Hlf!0.69!4.94!Hlf;;chrX:108009734..108009752,+!p2@Pou3f4!0.69!3.89!Pou3f4;;chr7:52960888..52960902,+!p7@Dbp!0.69!3.89!Dbp;;chr11:98603119..98603130,+!p2@Thra!0.68!37.15!Thra;;chrX:92906980..92907024,+!p2@Zc3h12b!0.68!10.64!Zc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+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006601,UBERON:0006777,UBERON:0010316
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 38: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011283
 |is_obsolete=
+|library_id=CNhs10501
+|library_id_phase_based=2:CNhs10501
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;16
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;16
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/corpora%2520quadrigemina%252c%2520adult.CNhs10501.16-22A4.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/corpora%2520quadrigemina%252c%2520adult.CNhs10501.16-22A4.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/corpora%2520quadrigemina%252c%2520adult.CNhs10501.16-22A4.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/corpora%2520quadrigemina%252c%2520adult.CNhs10501.16-22A4.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/corpora%2520quadrigemina%252c%2520adult.CNhs10501.16-22A4.mm9.nobarcode.rdna.fa.gz
 |name=corpora quadrigemina, adult
 |namespace=FANTOM5
@@ Line 43: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10501,LSID648,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.0532503644714875,0,0,0,0,0,-0.0014126706784584,0,0.0541042647168238,0,0,-0.0843392403965415,0,0,0,0,0.0303093843382358,0,0.0119992618872562,0,0,0,0,0,0.0606187686764715,0,0,0,0,0,0,0,-0.216330870700297,0,0,0,0,0.0465269389694287,0.0329387489569705,0.112517203338526,-0.0789858111573438,0.888219992473792,0.555690169062648,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0,0,0,0.0236693736272396,0.0398190537556165,-0.0321842802429986,0.557422433107953,0.0983479648072969,0,0.0262048012778499,0.135019174158258,0.0590140410331578,0,0,0.084886790756001,0.144058279896087,0.00569025171595694,0.0349718516247984,0,0,0,0,0,0,-0.0687933291582405,-0.259497577897227,-0.046467602012272,0.0334225037537722,0,0.805668224242234,0,0
 |rna_box=22
 |rna_catalog_number=
@@ Line 58: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 78: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:16-22A4;search_select_hide=table117:16-22A4
 }}

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FF:16-22A4: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:08, 4 June 2020

CNhs10501

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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