Difference between revisions of "FF:11849-124I4"

Latest revision as of 09:23, 4 June 2020

Name:	CD326+ enterocyte, pool2
Species:	Mouse (Mus musculus)
Library ID:	CNhs13197
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	Balb/c
tissue	ileum
dev stage	adult
sex	male
age	NA
cell type	enterocyte
cell line	NA
company	NA
collaboration	Shinji Fukuda (RCAI)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	Cont_Ep+_b
catalog number	NA
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00004678

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13197		CAGE		DRX008788		DRR009660

Accession ID Mm9

Library id		BAM		CTSS
CNhs13197		DRZ001085		DRZ002470

Accession ID Mm10

Library id		BAM		CTSS
CNhs13197		DRZ012435		DRZ013820

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

CNhs13197

MCL coexpression id	Coexpression dpi cluster scores median value
0	0
1	0
10	0
100	0
1000	--0.0355
1001	--0.0749
1002	--0.116
1003	--0.175
1004	0
1005	0.0745
1006	--0.317
1007	0.0722
1008	1.448
1009	--0.19
101	--0.51
1010	0
1011	--0.337
1012	0
1013	0.222
1014	--0.0874
1015	--0.584
1016	--0.488
1017	0
1018	0.478
1019	0
102	0
1020	0
1021	0.603
1022	--0.0704
1023	0
1024	--0.307
1025	0
1026	0
1027	--0.048
1028	0
1029	--0.115
103	--0.0887
1030	0
1031	-1.148
1032	0.896
1033	0.12
1034	0
1035	0
1036	0.196
1037	0
1038	0.415
1039	--0.0514
104	0
1040	--0.884
1041	0

Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family 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

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 this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon

link to dataset.
data

library id: CNhs13197

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0202
MA0003.1	MA0003.1	0.642
MA0004.1	MA0004.1	0.61
MA0006.1	MA0006.1	0.036
MA0007.1	MA0007.1	0.217
MA0009.1	MA0009.1	0.12
MA0014.1	MA0014.1	0.0535
MA0017.1	MA0017.1	8.60242e-40
MA0018.2	MA0018.2	0.00727
MA0019.1	MA0019.1	0.0886
MA0024.1	MA0024.1	1.46652e-4
MA0025.1	MA0025.1	0.299
MA0027.1	MA0027.1	0.279
MA0028.1	MA0028.1	0.237
MA0029.1	MA0029.1	0.85
MA0030.1	MA0030.1	0.275
MA0031.1	MA0031.1	0.0465
MA0035.2	MA0035.2	9.7584e-7
MA0038.1	MA0038.1	0.513
MA0039.2	MA0039.2	1.03939e-4
MA0040.1	MA0040.1	0.0917
MA0041.1	MA0041.1	0.158
MA0042.1	MA0042.1	0.219
MA0043.1	MA0043.1	0.338
MA0046.1	MA0046.1	6.84917e-49
MA0047.2	MA0047.2	0.0409
MA0048.1	MA0048.1	0.137
MA0050.1	MA0050.1	8.26523e-5
MA0051.1	MA0051.1	3.82717e-7
MA0052.1	MA0052.1	0.744
MA0055.1	MA0055.1	0.167
MA0057.1	MA0057.1	0.122
MA0058.1	MA0058.1	0.602
MA0059.1	MA0059.1	0.489
MA0060.1	MA0060.1	0.297
MA0061.1	MA0061.1	0.766
MA0062.2	MA0062.2	0.0137
MA0065.2	MA0065.2	1.09392e-17
MA0066.1	MA0066.1	0.193
MA0067.1	MA0067.1	0.198
MA0068.1	MA0068.1	0.125
MA0069.1	MA0069.1	0.758
MA0070.1	MA0070.1	0.611
MA0071.1	MA0071.1	0.00813
MA0072.1	MA0072.1	0.419
MA0073.1	MA0073.1	0.813
MA0074.1	MA0074.1	0.233
MA0076.1	MA0076.1	0.33
MA0077.1	MA0077.1	0.431
MA0078.1	MA0078.1	0.799
MA0079.2	MA0079.2	0.169
MA0080.2	MA0080.2	0.0643
MA0081.1	MA0081.1	0.451
MA0083.1	MA0083.1	0.549
MA0084.1	MA0084.1	0.286
MA0087.1	MA0087.1	0.357
MA0088.1	MA0088.1	0.501
MA0090.1	MA0090.1	0.908
MA0091.1	MA0091.1	0.0846
MA0092.1	MA0092.1	0.914
MA0093.1	MA0093.1	0.654
MA0099.2	MA0099.2	1.02887e-6
MA0100.1	MA0100.1	0.615
MA0101.1	MA0101.1	0.595
MA0102.2	MA0102.2	0.917
MA0103.1	MA0103.1	8.42809e-7
MA0104.2	MA0104.2	0.0541
MA0105.1	MA0105.1	0.0958
MA0106.1	MA0106.1	0.925
MA0107.1	MA0107.1	0.678
MA0108.2	MA0108.2	0.0425
MA0111.1	MA0111.1	0.616
MA0112.2	MA0112.2	0.0289
MA0113.1	MA0113.1	0.537
MA0114.1	MA0114.1	3.00312e-53
MA0115.1	MA0115.1	5.07003e-17
MA0116.1	MA0116.1	0.0911
MA0117.1	MA0117.1	0.0995
MA0119.1	MA0119.1	0.0613
MA0122.1	MA0122.1	0.564
MA0124.1	MA0124.1	0.591
MA0125.1	MA0125.1	0.691
MA0131.1	MA0131.1	0.845
MA0135.1	MA0135.1	0.103
MA0136.1	MA0136.1	0.00151
MA0137.2	MA0137.2	0.78
MA0138.2	MA0138.2	0.658
MA0139.1	MA0139.1	0.619
MA0140.1	MA0140.1	0.0219
MA0141.1	MA0141.1	1.42074e-10
MA0142.1	MA0142.1	0.0445
MA0143.1	MA0143.1	0.0647
MA0144.1	MA0144.1	0.0583
MA0145.1	MA0145.1	0.0134
MA0146.1	MA0146.1	0.066
MA0147.1	MA0147.1	0.0404
MA0148.1	MA0148.1	0.0203
MA0149.1	MA0149.1	0.0128
MA0150.1	MA0150.1	0.0334
MA0152.1	MA0152.1	0.0712
MA0153.1	MA0153.1	6.62693e-40
MA0154.1	MA0154.1	0.606
MA0155.1	MA0155.1	0.418
MA0156.1	MA0156.1	0.014
MA0157.1	MA0157.1	0.474
MA0159.1	MA0159.1	8.02461e-4
MA0160.1	MA0160.1	1.403e-7
MA0162.1	MA0162.1	0.487
MA0163.1	MA0163.1	0.417
MA0164.1	MA0164.1	0.613
MA0258.1	MA0258.1	0.0821
MA0259.1	MA0259.1	0.662

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 in 169 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: CNhs13197

Novel motif	Logo	P-value
1	1	0.284
10	10	0.498
100	100	0.569
101	101	0.804
102	102	0.69
103	103	0.807
104	104	0.823
105	105	0.338
106	106	0.0492
107	107	0.413
108	108	0.5
109	109	0.308
11	11	0.258
110	110	0.565
111	111	0.134
112	112	0.0482
113	113	0.187
114	114	0.0731
115	115	0.575
116	116	0.328
117	117	0.07
118	118	0.61
119	119	0.263
12	12	0.654
120	120	0.943
121	121	0.43
122	122	0.813
123	123	0.0378
124	124	0.113
125	125	0.427
126	126	0.103
127	127	0.628
128	128	0.0834
129	129	0.585
13	13	1.11912e-5
130	130	0.605
131	131	0.996
132	132	0.411
133	133	0.228
134	134	0.608
135	135	0.0661
136	136	0.00479
137	137	0.273
138	138	0.191
139	139	0.359
14	14	0.773
140	140	0.575
141	141	0.834
142	142	0.369
143	143	0.169
144	144	0.301
145	145	0.228
146	146	0.434
147	147	0.812
148	148	0.663
149	149	0.394
15	15	0.259
150	150	0.28
151	151	0.789
152	152	0.0641
153	153	0.574
154	154	0.671
155	155	0.323
156	156	0.145
157	157	0.477
158	158	0.332
159	159	0.572
160	160	0.325
161	161	0.831
162	162	0.851
163	163	0.12
164	164	0.256
165	165	0.948
166	166	0.443
167	167	0.837
168	168	0.739
169	169	0.198
17	17	0.0807
18	18	0.716
19	19	0.693
2	2	0.969
20	20	0.191
21	21	0.948
22	22	0.28
23	23	0.268
24	24	0.95
25	25	0.376
26	26	0.0377
27	27	0.545
28	28	0.31
29	29	0.448
3	3	0.333
30	30	0.325
31	31	0.949
32	32	0.499
33	33	0.207
34	34	0.807
35	35	0.77
36	36	0.851
37	37	0.0184
38	38	0.692
39	39	0.434
4	4	0.497
40	40	0.3
41	41	0.226
42	42	0.737
43	43	0.749
44	44	0.441
45	45	0.357
46	46	0.636
47	47	0.925
48	48	0.555
49	49	0.479
5	5	0.99
50	50	0.808
51	51	0.832
52	52	0.134
53	53	0.285
54	54	0.456
55	55	0.358
56	56	0.801
57	57	0.486
58	58	0.402
59	59	0.544
6	6	0.908
60	60	0.0348
61	61	0.704
62	62	0.301
63	63	0.365
64	64	0.914
65	65	0.459
66	66	0.586
67	67	0.183
68	68	0.0345
69	69	0.827
7	7	0.0496
70	70	0.0197
71	71	0.328
72	72	0.643
73	73	0.0134
74	74	0.727
75	75	0.0674
76	76	0.753
77	77	0.168
78	78	0.014
79	79	0.794
8	8	0.996
80	80	0.867
81	81	0.804
82	82	0.2
83	83	0.657
84	84	0.0264
85	85	0.193
86	86	0.0785
87	87	0.00975
88	88	0.303
89	89	0.738
9	9	0.665
90	90	0.822
91	91	0.719
92	92	0.939
93	93	0.174
94	94	0.279
95	95	0.0702
96	96	0.679
97	97	0.901
98	98	0.964
99	99	0.897

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: CNhs13197

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011149 mouse CD326-positive enterocyte 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)
0000548 (animal cell)
0000075 (columnar/cuboidal epithelial cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0002563 (intestinal epithelial cell)
0000255 (eukaryotic cell)
0000239 (brush border epithelial cell)
0000677 (gut absorptive cell)
0000212 (absorptive cell)
0002076 (endo-epithelial cell)
0002251 (epithelial cell of alimentary canal)
0000584 (enterocyte)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000160 (intestine)
0000483 (epithelium)
0001242 (intestinal mucosa)
0000479 (tissue)
0001007 (digestive system)
0000344 (mucosa)
0000064 (organ part)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0005911 (endo-epithelium)
0004923 (organ component layer)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0000060 (anatomical wall)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0000490 (unilaminar epithelium)
0001262 (wall of intestine)
0004786 (gastrointestinal system mucosa)
0000485 (simple columnar epithelium)
0003350 (epithelium of mucosa)
0003929 (gut epithelium)
0004808 (gastrointestinal system epithelium)
0001277 (intestinal epithelium)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0011149 (mouse CD326-positive enterocyte 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:0000223 (endodermal cell)

@@ Line 1: / Line 1: @@
 {{f5samples
 |DRA_sample_Accession=CAGE@SAMD00004678
-|accession_numbers=CAGE;DRX008788;DRR009660;DRZ001085;DRZ002470
+|accession_numbers=CAGE;DRX008788;DRR009660;DRZ001085;DRZ002470;DRZ012435;DRZ013820
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000160,UBERON:0000483,UBERON:0001242,UBERON:0000479,UBERON:0001007,UBERON:0000344,UBERON:0000064,UBERON:0004119,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0005911,UBERON:0004923,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0000060,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0000490,UBERON:0001262,UBERON:0004786,UBERON:0000485,UBERON:0003350,UBERON:0003929,UBERON:0004808,UBERON:0001277,UBERON:0010317,UBERON:0001555,UBERON:0005409
 |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000075,CL:0000066,CL:0002371,CL:0002563,CL:0000255,CL:0000239,CL:0000677,CL:0000212,CL:0002076,CL:0002251,CL:0000584
@@ Line 46: / Line 46: @@
 |library_id=CNhs13197
 |library_id_phase_based=2:CNhs13197
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11849
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11849
 |mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD326%252b%2520enterocyte%252c%2520pool2.CNhs13197.11849-124I4.mm10.nobarcode.bam
 |mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD326%252b%2520enterocyte%252c%2520pool2.CNhs13197.11849-124I4.mm10.nobarcode.ctss.bed.gz
@@ Line 93: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11849-124I4;search_select_hide=table117:11849-124I4
 }}

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