FF:12158-128G7: Difference between revisions

Latest revision as of 18:32, 4 June 2020

Name:	Atoh+ Inner ear hair cells - organ of corti, pool1
Species:	Mouse (Mus musculus)
Library ID:	CNhs12533
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	organ of corti
dev stage	NA
sex	mixed
age	NA
cell type	hair cell, organ of corti, inner
cell line	NA
company	NA
collaboration	Albert Edge (Department of Otolaryngology, Harvard Medical School)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

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

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005207

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12533		CAGE		DRX008761		DRR009633

Accession ID Mm9

Library id		BAM		CTSS
CNhs12533		DRZ001058		DRZ002443

Accession ID Mm10

Library id		BAM		CTSS
CNhs12533		DRZ012408		DRZ013793

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

CNhs12533

0	0
1	0.073
10	0
100	0.0645
1000	0
1001	-0.0749
1002	0.246
1003	-0.0306
1004	0
1005	0
1006	0.113
1007	0.246
1008	0
1009	0.168
101	-0.0178
1010	0
1011	0.0288
1012	0
1013	-0.00408
1014	-0.0874
1015	0.239
1016	0.31
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	0.0503
1023	0
1024	0
1025	0
1026	0
1027	0.237
1028	0
1029	-0.176
103	-0.0142
1030	0
1031	0.435
1032	0.203
1033	0.00678
1034	0
1035	0
1036	0.0695
1037	0.121
1038	0.047
1039	0.00983
104	0
1040	-0.0382
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: CNhs12533This sample isn't target for the analysis

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: CNhs12533This sample isn't target for the analysis

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: CNhs12533

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000265 mouse Atoh-positive inner hair 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)
0000197 (receptor cell)
0000540 (neuron)
0000003 (native cell)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0002319 (neural cell)
0000393 (electrically responsive cell)
0000006 (neuronal receptor cell)
0002374 (ear hair cell)
0002491 (auditory epithelial cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0000202 (auditory hair cell)
0000199 (mechanoreceptor cell)
0000098 (sensory epithelial cell)
0000855 (sensory hair cell)
0000589 (cochlear inner hair cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001474 (bone element)
0000033 (head)
0000058 (duct)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000020 (sense organ)
0000075 (subdivision of skeletal system)
0004765 (skeletal element)
0004766 (cranial bone)
0008193 (pneumatized bone)
0005913 (zone of bone organ)
0005744 (cranial conduit)
0001032 (sensory system)
0003457 (head bone)
0008001 (irregular bone)
0007914 (head or neck bone)
0010317 (germ layer / neural crest derived structure)
0002227 (spiral organ of cochlea)
0001846 (internal ear)
0000153 (anterior region of body)
0007811 (craniocervical region)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0004456 (entire sense organ system)
0004339 (calvarium)
0002105 (vestibulo-auditory system)
0001678 (temporal bone)
0003128 (cranium)
0001694 (petrous part of temporal bone)
0004681 (vestibular system)
0001839 (bony labyrinth)
0001690 (ear)
0001844 (cochlea)
0001849 (membranous labyrinth)
0002499 (cochlear labyrinth)
0001855 (cochlear duct of membranous labyrinth)
0011137 (axial skeletal system)
0010323 (cranial skeletal system)
0003129 (skull)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000264 (mouse inner hair cell sample)
0000265 (mouse Atoh-positive inner hair 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:0000031 (neuroblast)
CL:0000221 (ectodermal cell)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000020,UBERON:0000032,UBERON:0000033,UBERON:0000058,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000073,UBERON:0000075,UBERON:0000153,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000914,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000926,UBERON:0001016,UBERON:0001017,UBERON:0001032,UBERON:0001062,UBERON:0001434,UBERON:0001474,UBERON:0001678,UBERON:0001690,UBERON:0001694,UBERON:0001703,UBERON:0001839,UBERON:0001844,UBERON:0001846,UBERON:0001849,UBERON:0001855,UBERON:0002050,UBERON:0002105,UBERON:0002204,UBERON:0002227,UBERON:0002241,UBERON:0002329,UBERON:0002342,UBERON:0002346,UBERON:0002499,UBERON:0002532,UBERON:0003059,UBERON:0003075,UBERON:0003077,UBERON:0003089,UBERON:0003104,UBERON:0003128,UBERON:0003129,UBERON:0003457,UBERON:0003465,UBERON:0004111,UBERON:0004120,UBERON:0004121,UBERON:0004288,UBERON:0004456,UBERON:0004681,UBERON:0004765,UBERON:0004766,UBERON:0005291,UBERON:0005423,UBERON:0005743,UBERON:0005744,UBERON:0005944,UBERON:0006598,UBERON:0007284,UBERON:0008001,UBERON:0008193,UBERON:0009142
+|DRA_sample_Accession=CAGE@SAMD00005207
-|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000006,CL:0000012,CL:0000031,CL:0000034,CL:0000047,CL:0000048,CL:0000055,CL:0000063,CL:0000066,CL:0000098,CL:0000133,CL:0000144,CL:0000197,CL:0000199,CL:0000202,CL:0000211,CL:0000220,CL:0000221,CL:0000255,CL:0000393,CL:0000404,CL:0000540,CL:0000548,CL:0000589,CL:0000723,CL:0000855,CL:0002319,CL:0002321,CL:0002371,CL:0002374,CL:0002491
+|accession_numbers=CAGE;DRX008761;DRR009633;DRZ001058;DRZ002443;DRZ012408;DRZ013793
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001474,UBERON:0000033,UBERON:0000058,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000020,UBERON:0000075,UBERON:0004765,UBERON:0004766,UBERON:0008193,UBERON:0005913,UBERON:0005744,UBERON:0001032,UBERON:0003457,UBERON:0008001,UBERON:0007914,UBERON:0010317,UBERON:0002227,UBERON:0001846,UBERON:0000153,UBERON:0007811,UBERON:0002204,UBERON:0001434,UBERON:0004456,UBERON:0004339,UBERON:0002105,UBERON:0001678,UBERON:0003128,UBERON:0001694,UBERON:0004681,UBERON:0001839,UBERON:0001690,UBERON:0001844,UBERON:0001849,UBERON:0002499,UBERON:0001855,UBERON:0011137,UBERON:0010323,UBERON:0003129
+|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000197,CL:0000540,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0002319,CL:0000393,CL:0000006,CL:0002374,CL:0002491,CL:0000211,CL:0000404,CL:0000255,CL:0000202,CL:0000199,CL:0000098,CL:0000855,CL:0000589
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000264,FF:0000265
 |comment=Previously: Math1- Inner ear hair cells - organ of corti, pool1
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chrX:108009761..108009788,+!p1@Pou3f4!2.39!245.35!Pou3f4;;chr12:86814833..86814846,+!p1@Fos!2.22!3572.44!Fos;;chr7:19895354..19895369,-!p1@Fosb!2.15!190.10!Fosb;;chr7:19895384..19895399,-!p2@Fosb!2.05!153.26!Fosb;;chr9:87626083..87626108,-!p1@Tbx18!1.97!198.26!Tbx18;;chrX:108009798..108009815,+!p3@Pou3f4!1.93!84.08!Pou3f4;;chr12:74147689..74147711,-!p1@Six1!1.92!172.96!Six1;;chr18:42554216..42554229,+!p1@Pou4f3!1.86!71.27!Pou4f3;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.81!78.79!Pou3f3;;chr14:122874619..122874634,+!p1@Zic2!1.69!47.88!Zic2;;chr18:35020854..35020869,+!p1@Egr1!1.66!1604.37!Egr1;;chr13:31717548..31717596,+!p1@Foxf2!1.66!86.32!Foxf2;;chr10:67000609..67000625,+!p1@Egr2!1.64!95.29!Egr2;;chr15:101097270..101097290,+!p1@Nr4a1!1.53!324.78!Nr4a1;;chrX:108009734..108009752,+!p2@Pou3f4!1.49!29.95!Pou3f4;;chr17:86087592..86087615,-!p1@Six2!1.45!26.91!Six2;;chr15:78994907..78994926,-!p1@Sox10!1.44!67.10!Sox10;;chr8:94325321..94325366,-!p1@Irx3!1.43!60.86!Irx3;;chr3:34548909..34548927,+!p1@Sox2!1.43!42.92!Sox2;;chr1:173987720..173987729,-!p1@Nhlh1!1.40!24.18!Nhlh1;;chr2:9800207..9800234,-!p1@Gata3!1.39!69.99!Gata3;;chr6:64679112..64679126,+!p1@Atoh1!1.38!23.06!Atoh1;;chr8:87502608..87502623,-!p1@Junb!1.37!354.73!Junb;;chr12:34642510..34642530,+!p1@Twist1!1.37!70.15!Twist1;;chr18:42554021..42554024,+!p2@Pou4f3!1.34!20.98!Pou4f3;;chr3:130813736..130813752,+!p3@Lef1!1.31!27.07!Lef1;;chr8:94881872..94881887,+!p2@Irx5!1.30!20.50!Irx5;;chr9:87625971..87625992,-!p2@Tbx18!1.30!19.06!Tbx18;;chr2:26062055..26062100,-!p1@Lhx3!1.28!17.94!Lhx3;;chr8:94325486..94325510,-!p4@Irx3!1.25!21.94!Irx3;;chr13:72766279..72766296,+!p2@Irx2!1.24!24.50!Irx2;;chr4:94718861..94718872,-!p2@Jun!1.23!117.71!Jun;;chr1:193007123..193007139,-!p1@Atf3!1.22!86.64!Atf3;;chr4:154335024..154335039,+!p1@Hes5!1.22!18.74!Hes5;;chr13:72101161..72101177,-!p2@Irx1!1.20!20.34!Irx1;;chr4:94718879..94718898,-!p1@Jun!1.19!1031.20!Jun;;chr2:9809357..9809371,-!p2@Gata3!1.18!14.09!Gata3;;chr9:55388997..55389016,+!p1@Isl2!1.18!14.09!Isl2;;chr5:138199361..138199441,+!p2@Tsc22d4!1.17!25.94!Tsc22d4;;chr8:94881733..94881790,+!p1@Irx5!1.16!26.58!Irx5;;chr13:31898496..31898519,+!p3@Foxc1!1.15!21.30!Foxc1;;chr13:72101178..72101203,-!p1@Irx1!1.15!20.50!Irx1;;chr2:28771380..28771413,-!p2@Barhl1!1.15!13.13!Barhl1;;chr13:31898637..31898653,+!p2@Foxc1!1.12!21.94!Foxc1;;chr4:99322820..99322845,+!p1@Foxd3!1.11!15.05!Foxd3;;chr8:94325273..94325288,-!p5@Irx3!1.10!14.25!Irx3;;chr13:117099847..117099907,-!p1@Isl1!1.09!20.82!Isl1;;chr8:24780125..24780143,+!p1@Zmat4!1.09!16.50!Zmat4;;chr4:55545337..55545357,-!p1@Klf4!1.08!164.63!Klf4;;chr13:72101141..72101158,-!p3@Irx1!1.08!13.93!Irx1;;chr18:52775562..52775650,+!p1@Zfp474!1.08!11.05!Zfp474;;chr13:31898767..31898785,+!p4@Foxc1!1.06!12.81!Foxc1;;chr13:31717597..31717613,+!p2@Foxf2!1.06!10.41!Foxf2;;chr4:97248607..97248649,+!p15@Nfia!1.06!10.41!Nfia;;chr13:31898729..31898761,+!p1@Foxc1!1.03!24.18!Foxc1;;chr13:72766250..72766273,+!p1@Irx2!1.03!15.05!Irx2;;chr4:48058047..48058062,+!p1@Nr4a3!1.03!15.05!Nr4a3;;chr13:78339428..78339466,-!p2@Nr2f1!1.00!12.33!Nr2f1;;chr19:59533221..59533271,+!p1@Emx2!1.00!11.05!Emx2;;chr14:118636214..118636235,-!p1@Sox21!0.99!10.57!Sox21;;chr13:99124189..99124205,+!p1@Foxd1!0.98!13.29!Foxd1;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!0.98!11.05!Zbtb11;;chr3:34548946..34548972,+!p2@Sox2!0.98!9.45!Sox2;;chr15:76287876..76287894,+!p1@Scx!0.96!45.80!Scx;;chr8:94325814..94325839,-!p2@Irx3!0.95!16.98!Irx3;;chr13:78339134..78339185,-!p5@Nr2f1!0.95!9.93!Nr2f1;;chr14:122874593..122874610,+!p2@Zic2!0.94!7.69!Zic2;;chr14:17407878..17407926,-!p1@Rarb!0.93!17.30!Rarb;;chr12:74147860..74147888,-!p2@Six1!0.93!7.53!Six1;;chr9:62996985..62996990,-!p1@Skor1!0.93!7.53!Skor1;;chr5:102094214..102094230,-!p1@Nkx6-1!0.93!7.53!Nkx6-1;;chr18:42554126..42554135,+!p3@Pou4f3!0.92!7.37!Pou4f3;;chr11:116196664..116196679,-!p1@Foxj1!0.91!11.21!Foxj1;;chr2:70313168..70313184,+!p1@Sp5!0.90!10.57!Sp5;;chr4:97248652..97248671,+!p19@Nfia!0.88!6.57!Nfia;;chr10:30375579..30375616,-!p3@Ncoa7!0.87!15.69!Ncoa7;;chr4:82351639..82351658,-!p14@Nfib!0.87!6.41!Nfib;;chr12:28027561..28027591,-!p1@Sox11!0.86!43.08!Sox11;;chr8:94325847..94325869,-!p3@Irx3!0.86!10.41!Irx3;;chr13:78339476..78339515,-!p1@Nr2f1!0.86!9.77!Nr2f1;;chr18:7004715..7004731,-!p1@Mkx!0.85!15.21!Mkx;;chr4:154010409..154010466,-!p2@Prdm16!0.85!14.89!Prdm16;;chr2:168427252..168427273,-!p2@Nfatc2!0.85!7.69!Nfatc2;;chr13:78339382..78339420,-!p3@Nr2f1!0.85!7.21!Nr2f1;;chr8:94325446..94325459,-!p8@Irx3!0.85!6.57!Irx3;;chr18:81183755..81183761,-!p1@Sall3!0.85!6.09!Sall3;;chr2:9809374..9809396,-!p4@Gata3!0.85!6.09!Gata3;;chr2:9809402..9809422,-!p5@Gata3!0.84!5.93!Gata3;;chr17:25707623..25707639,-!p1@Sox8!0.83!26.42!Sox8;;chr4:135699731..135699747,+!p1@Id3!0.82!673.75!Id3;;chr11:44431687..44431706,+!p2@Ebf1!0.82!28.19!Ebf1;;chr15:79178060..79178074,+!p2@Maff!0.82!7.53!Maff;;chr8:123640063..123640077,+!p1@Foxc2!0.81!10.25!Foxc2;;chr18:35020615.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Yy1;;chr17:51952617..51952680,-!p3@Satb1!0.28!8.01!Satb1;;chr5:65194810..65194819,+!p9@Klf3!0.28!2.56!Klf3;;chr12:3891810..3891829,+!p2@Dnmt3a!0.28!1.92!Dnmt3a;;chr2:156666727..156666753,+!p2@Tgif2!0.28!1.76!Tgif2;;chr6:53523346..53523353,+!p3@Creb5!0.28!1.60!Creb5;;chrX:34442872..34442899,-!p1@Nkrf!0.28!1.44!Nkrf;;chr3:130815703..130815721,+!p2@Lef1!0.28!1.28!Lef1;;chr11:121380611..121380625,-!p3@Zfp750!0.28!1.28!Zfp750;;chr8:72662954..72662961,-!p5@LOC100048268,p5@Rfxank!0.28!1.12!Rfxank;;chr16:15887371..15887385,+!p1@Cebpd!0.27!56.85!Cebpd;;chr9:19426523..19426584,+!p1@Zfp317!0.27!24.66!Zfp317;;chr7:48888915..48888973,+!p1@Zfp788!0.27!20.98!Zfp788;;chr15:81575569..81575599,+!p2@Zc3h7b!0.27!17.94!Zc3h7b;;chr7:5003117..5003159,+!p1@Zfp580!0.27!12.01!Zfp580;;chr17:32526309..32526356,-!p2@Wiz!0.27!8.33!Wiz;;chr18:83084030..83084056,+!p1@Zfp516!0.27!7.85!Zfp516;;chr8:125778131..125778178,+!p1@Zfp276!0.27!7.05!Zfp276;;chr4:133309531..133309581,-!p4@Arid1a!0.27!6.25!Arid1a;;chr14:52634536..52634572,-!p4@Zfp219!0.27!4.32!Zfp219;;chr8:108160826..108160879,+!p3@Ctcf!0.27!4.16!Ctcf;;chr11:59285966..59285990,-!p2@Zfp867!0.27!3.52!Zfp867;;chr16:42907656..42907675,+!p10@Zbtb20!0.27!2.88!Zbtb20;;chr12:3806962..3806973,+!p6@Dnmt3a!0.27!2.40!Dnmt3a;;chr19:9016651..9016662,+!p3@Mta2!0.27!2.40!Mta2;;chr10:67375146..67375208,-!p2@Zfp365!0.27!1.76!Zfp365;;chr4:122911056..122911065,+!p2@Heyl!0.27!1.76!Heyl;;chr4:55545051..55545110,-!p2@Klf4!0.27!1.28!Klf4;;chr3:95032184..95032195,-!p4@Mllt11!0.27!1.28!Mllt11;;chr9:96159116..96159130,+!p6@Tfdp2!0.27!1.28!Tfdp2;;chr14:76904313..76904328,+!p1@Tsc22d1!0.26!320.78!Tsc22d1;;chr4:154597177..154597195,-!p1@Ski!0.26!61.98!Ski;;chr2:91864661..91864686,-!p1@Creb3l1!0.26!35.07!Creb3l1;;chr1:170362040..170362113,-!p2@Pbx1!0.26!12.17!Pbx1;;chr17:34169016..34169068,+!p2@Rxrb!0.26!11.37!Rxrb;;chr1:191994550..191994623,-!p1@Prox1!0.26!10.73!Prox1;;chr3:135354476..135354528,-!p2@Nfkb1!0.26!8.49!Nfkb1;;chr5:139060892..139060911,-!p2@Zfp68!0.26!7.37!Zfp68;;chr17:23004042..23004077,-!p2@Zfp945!0.26!5.61!Zfp945;;chr14:22319053..22319105,+!p2@Myst4!0.26!4.80!Myst4;;chr8:111227738..111227793,+!p@chr8:111227738..111227793,+!0.26!3.36!Zfhx3;;chr7:77511311..77511352,-!p4@Nr2f2!0.26!2.56!Nr2f2;;chr8:72356384..72356434,+!p2@Pbx4!0.26!1.76!Pbx4;;chr17:37139455..37139469,+!p3@Zfp57!0.26!1.76!Zfp57;;chr7:91558631..91558652,-!p3@Arnt2!0.26!1.60!Arnt2;;chr12:109242296..109242307,-!p3@Bcl11b!0.26!1.60!Bcl11b;;chr9:71958979..71959032,-!p4@Tcf12!0.26!1.28!Tcf12;;chr14:52640315..52640328,-!p10@Zfp219!0.26!1.28!Zfp219;;chr10:67599450..67599456,-!p8@Arid5b!0.26!1.12!Arid5b;;chr16:43510301..43510313,+!p24@Zbtb20!0.26!1.12!Zbtb20;;chr7:52960780..52960793,+!p5@Dbp!0.26!1.12!Dbp;;chr7:122968213..122968266,-!p4@Sox6!0.26!1.12!Sox6;;chr6:14851377..14851396,+!p10@Foxp2!0.26!0.80!Foxp2;;chr6:144157991..144158007,-!p9@Sox5!0.26!0.80!Sox5;;chr5:42155788..42155800,-!p1@Nkx3-2!0.26!0.80!Nkx3-2;;chr7:147234982..147234988,-!p1@Msx3!0.26!0.80!Msx3;;chr10:126778639..126778670,-!p3@Gli1!0.26!0.80!Gli1;;chr13:56804798..56804806,+!p7@Smad5!0.26!0.80!Smad5;;chr14:98568502..98568516,-!p7@Dach1!0.26!0.80!Dach1;;chr12:50483639..50483654,+!p1@Foxg1!0.26!0.80!Foxg1;;chr14:49287186..49287225,-!p1@Otx2!0.26!0.80!Otx2;;chr12:75002389..75002406,+!p4@Hif1a!0.26!0.80!Hif1a;;chr13:78338032..78338049,-!p8@Nr2f1!0.26!0.80!Nr2f1;;chr12:50485973..50486015,+!p2@Foxg1!0.26!0.80!Foxg1;;chr15:76353005..76353021,-!p2@Scrt1!0.26!0.80!Scrt1;;chr14:17407857..17407875,-!p4@Rarb!0.26!0.80!Rarb;;chr13:78337076..78337111,-!p18@Nr2f1!0.26!0.80!Nr2f1;;chr2:77541432..77541474,-!p5@Zfp385b!0.26!0.80!Zfp385b;;chr4:97248379..97248387,+!p29@Nfia!0.26!0.80!Nfia;;chr3:34549096..34549111,+!p3@Sox2!0.26!0.80!Sox2;;chr2:71384458..71384526,-!p2@Dlx2!0.26!0.80!Dlx2;;chr4:99323046..99323073,+!p3@Foxd3!0.26!0.80!Foxd3;;chr3:34548845..34548856,+!p4@Sox2!0.26!0.80!Sox2;;chr4:154010313..154010324,-!p9@Prdm16!0.26!0.80!Prdm16;;chr1:169528581..169528607,+!p7@Rxrg!0.26!0.80!Rxrg;;chr2:30701003..30701028,+!p6@Prrx2!0.26!0.80!Prrx2;;chr2:164228702..164228719,+!p1@Rbpjl!0.26!0.80!Rbpjl;;chr1:194979383..194979393,+!p3@Irf6!0.26!0.80!Irf6;;chr9:106355745..106355766,+!p7@Pcbp4!0.26!0.80!Pcbp4;;chr9:63869510..63869530,-!p10@Smad6!0.26!0.80!Smad6;;chr16:55819071..55819073,-!p11@Nfkbiz!0.26!0.80!Nfkbiz;;chr16:18587052..18587063,-!p3@Tbx1!0.26!0.80!Tbx1;;chr12:25780945..25780961,-!p1@Id2!0.25!269.53!Id2;;chr12:99985145..99985256,+!p1@Zc3h14!0.25!53.65!Zc3h14;;chr5:77694479..77694574,+!p1@Rest!0.25!34.27!Rest;;chr5:72950853..72950930,-!p1@Nfxl1!0.25!27.39!Nfxl1;;chr7:148513456..148513506,-!p1@Deaf1!0.25!24.66!Deaf1;;chr10:79862175..79862221,-!p1@Mbd3!0.25!21.78!Mbd3;;chr12:9581262..9581282,+!p1@Osr1!0.25!18.90!Osr1;;chr1:135320989..135321043,-!p1@Sox13!0.25!16.98!Sox13;;chr12:25336211..25336274,+!p1@Klf11!0.25!16.18!Klf11;;chr9:20189534..20189590,-!p1@Zfp560!0.25!15.69!Zfp560;;chr8:107694628..107694659,+!p1@Cbfb!0.25!13.61!Cbfb;;chr4:97439116..97439202,+!p5@Nfia!0.25!13.61!Nfia;;chr7:88005795..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+|ffid_belonging_in_development=CL:0000133,CL:0000031,CL:0000221
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 36: / Line 42: @@
 |has_quality=
 |id=FF:12158-128G7
-|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0000265
+|is_a=EFO:0002091;;FF:0000265
+|is_obsolete=
+|library_id=CNhs12533
+|library_id_phase_based=2:CNhs12533
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;12158
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;12158
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/Atoh1%252b%2520Inner%2520ear%2520hair%2520cells%2520-%2520organ%2520of%2520corti%252c%2520pool1.CNhs12533.12158-128G7.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/Atoh1%252b%2520Inner%2520ear%2520hair%2520cells%2520-%2520organ%2520of%2520corti%252c%2520pool1.CNhs12533.12158-128G7.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/Atoh1%252b%2520Inner%2520ear%2520hair%2520cells%2520-%2520organ%2520of%2520corti%252c%2520pool1.CNhs12533.12158-128G7.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/Atoh1%252b%2520Inner%2520ear%2520hair%2520cells%2520-%2520organ%2520of%2520corti%252c%2520pool1.CNhs12533.12158-128G7.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/Atoh1%252b%2520Inner%2520ear%2520hair%2520cells%2520-%2520organ%2520of%2520corti%252c%2520pool1.CNhs12533.12158-128G7.mm9.nobarcode.rdna.fa.gz
 |name=Atoh+ Inner ear hair cells - organ of corti, pool1
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12533,LSID919,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.11779559634038,0,0,0,0,0,-0.184498165558865,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.127379638095999,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.200261185318516,0,0,0,0,0.0118700468626334,0.0221005965958263,0.115949209558817,-0.0127678977495094,-0.813818636773006,0.145353267573864,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0.064513712786576,0,0,0,-0.0428469550828748,0,-0.0433199442101295,0,0,0,-0.0747164040954423,0.0158985965953375,0.200070564234433,-0.0365927089968535,0,0,0.0643365401291827,0,0,0,0.0186432380827105,0.0615692006790834,-0.531401167953994,-0.0788315948399074,0,0,0,0,0,0.064513712786576,-0.192380528288829,-0.522081935444182,-0.14913113740742,0,0,0,0,0
 |rna_box=128
 |rna_catalog_number=
@@ Line 57: / Line 76: @@
 |rna_weight_ug=0.5
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 76: / Line 96: @@
 |sample_tissue=organ of corti
 |top_motifs=ADNP_IRX_SIX_ZHX:3.3383391087;FOXN1:2.32853303511;PDX1:2.30523891917;LHX3,4:2.15775376045;POU6F1:2.11585993782;FOXO1,3,4:1.72627968354;FOXD3:1.70597833792;MYBL2:1.67652348432;SP1:1.66095053001;HIF1A:1.65921065764;PAX8:1.64308382958;HES1:1.64168964735;SOX2:1.55013963973;HMGA1,2:1.41386917771;PAX6:1.33758785107;STAT5{A,B}:1.2531355253;SOX5:1.23207120524;EBF1:1.18484775677;MTE{core}:1.14151811116;TBX4,5:1.13781261768;LEF1_TCF7_TCF7L1,2:1.13530704905;NKX2-1,4:1.12921116833;BPTF:1.12754283869;ATF4:1.09803761103;GCM1,2:1.09043284798;GFI1:1.05190614785;SMAD1..7,9:1.04628922578;HBP1_HMGB_SSRP1_UBTF:1.01924850087;MAZ:1.01726793106;RFX1:1.01589448271;NANOG:0.998987074642;DMAP1_NCOR{1,2}_SMARC:0.990539482942;SOX{8,9,10}:0.985481110436;ZFP161:0.983927986364;TFAP2B:0.975418967208;IKZF1:0.964713069939;HIC1:0.958969237299;GTF2A1,2:0.956834780516;PAX5:0.932915147649;PATZ1:0.894502354551;MED-1{core}:0.88879474513;STAT1,3:0.878954702258;YY1:0.871745776043;CREB1:0.864842904752;POU2F1..3:0.860113240198;RFX2..5_RFXANK_RFXAP:0.853365751167;KLF4:0.837024363275;XCPE1{core}:0.830447531345;EGR1..3:0.825620289862;FOXP3:0.819504733692;CDC5L:0.806999902784;FOSL2:0.796281624325;DBP:0.780941613485;NKX3-1:0.776299766104;NKX6-1,2:0.773628378291;ONECUT1,2:0.759563441598;TLX1..3_NFIC{dimer}:0.755481926589;JUN:0.696972801588;OCT4_SOX2{dimer}:0.69113951218;HMX1:0.689642695385;NANOG{mouse}:0.677742371399;EN1,2:0.663319754148;BREu{core}:0.654473405064;ATF5_CREB3:0.642861965588;ZNF384:0.61759438157;AR:0.61435502038;REST:0.609557685616;ELK1,4_GABP{A,B1}:0.608295406497;VSX1,2:0.59572232099;HOX{A4,D4}:0.591859992842;GZF1:0.577934186007;SPZ1:0.57511655054;POU5F1:0.574242757751;FOX{I1,J2}:0.562024609517;HSF1,2:0.558818498419;NRF1:0.542887896778;SOX17:0.503680766064;ZIC1..3:0.502731894605;CDX1,2,4:0.495733255382;ZNF143:0.491238611886;ATF6:0.485619607895;EP300:0.482052858569;NFY{A,B,C}:0.481840038366;GTF2I:0.48064042652;MYFfamily:0.41501917111;SNAI1..3:0.409904637649;TEF:0.36946303966;TFAP2{A,C}:0.363256835087;ZNF238:0.330070306101;RORA:0.327433171507;FOXQ1:0.3062085245;ALX1:0.282511335841;NHLH1,2:0.282246859402;RREB1:0.27446319021;TFDP1:0.267123565372;NR3C1:0.264917702361;TFAP4:0.242713348655;MAFB:0.238748607437;MZF1:0.233870387088;LMO2:0.21623868718;NFIL3:0.210526858732;FOXL1:0.206346601317;MYOD1:0.204440231356;GFI1B:0.195357544232;PRDM1:0.195327860964;TOPORS:0.194866222586;POU3F1..4:0.167685296813;PRRX1,2:0.145776118145;FOXP1:0.12574729549;MTF1:0.116044201453;CRX:0.11397576274;ATF2:0.100086109833;NKX2-3_NKX2-5:0.0943530551499;NFATC1..3:0.0865936962852;NFIX:0.0819419202403;TEAD1:0.0774069565101;TGIF1:0.0695320825372;ZEB1:0.0651188258359;IKZF2:0.0622887559621;FOX{D1,D2}:0.0533370524769;ZBTB6:0.0371023338762;AHR_ARNT_ARNT2:-0.0248082793362;HLF:-0.0256359117634;CUX2:-0.0438848542488;TFCP2:-0.0600440962305;ESR1:-0.079372114492;PAX4:-0.0898920764691;PPARG:-0.0976819082833;SREBF1,2:-0.115318549503;PAX2:-0.130941947929;TBP:-0.132297919613;PAX1,9:-0.144071753779;TAL1_TCF{3,4,12}:-0.157458140172;NKX2-2,8:-0.158879043749;RXR{A,B,G}:-0.165452461783;SRF:-0.171189307299;MYB:-0.23011201532;MEF2{A,B,C,D}:-0.245708984309;ZBTB16:-0.306122435078;HAND1,2:-0.310729349764;STAT2,4,6:-0.313807196797;BACH2:-0.31630642894;RUNX1..3:-0.369625369381;NFKB1_REL_RELA:-0.370498096786;FOX{F1,F2,J1}:-0.375958124118;FOXA2:-0.387516739695;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.40145710878;ELF1,2,4:-0.409266608926;GATA4:-0.413320818292;SPI1:-0.421150165077;UFEwm:-0.423179770824;E2F1..5:-0.425772379148;IRF7:-0.455613878268;FOXM1:-0.471816771275;PBX1:-0.500193722706;CEBPA,B_DDIT3:-0.506810242223;SPIB:-0.516916765711;GLI1..3:-0.518520343796;HOX{A5,B5}:-0.525739498712;FOS_FOS{B,L1}_JUN{B,D}:-0.535414086022;ETS1,2:-0.544904024789;IRF1,2:-0.565743544342;NFE2L1:-0.570379620382;AIRE:-0.576575692709;NR5A1,2:-0.604547782748;HNF1A:-0.610706183698;HNF4A_NR2F1,2:-0.653614493768;ARID5B:-0.655716152324;NFE2L2:-0.665235594841;RBPJ:-0.672067372622;T:-0.689831732089;GATA6:-0.709910717856;bHLH_family:-0.73373418993;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.755561821325;TP53:-0.78472030278;ZNF423:-0.793950772607;HOXA9_MEIS1:-0.822499755559;ESRRA:-0.826811119849;ZNF148:-0.971796277662;PITX1..3:-1.02455161033;EVI1:-1.07441364905;RXRA_VDR{dimer}:-1.12223030273;NR1H4:-1.13172783477;NR6A1:-1.22718969893;NFE2:-1.24533232996;POU1F1:-1.3870811695;ALX4:-1.48397975788;TLX2:-1.52122555357;NKX3-2:-1.97723657318
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:12158-128G7;search_select_hide=table117:12158-128G7
 }}

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FF:12158-128G7: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:32, 4 June 2020

CNhs12533

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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