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{{f5samples
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002100,UBERON:0000483,UBERON:0001474,UBERON:0000033,UBERON:0000926,UBERON:0000479,UBERON:0000058,UBERON:0000064,UBERON:0000073,UBERON:0004121,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0004765,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0000477,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0000119,UBERON:0000490,UBERON:0005291,UBERON:0000020,UBERON:0000075,UBERON:0000485,UBERON:0003465,UBERON:0008193,UBERON:0000032,UBERON:0005744,UBERON:0003104,UBERON:0001032,UBERON:0000914,UBERON:0008001,UBERON:0005085,UBERON:0007497,UBERON:0009955,UBERON:0003067,UBERON:0002546,UBERON:0005256,UBERON:0001048,UBERON:0007914,UBERON:0003457,UBERON:0004766,UBERON:0006598,UBERON:0005253,UBERON:0002532,UBERON:0001017,UBERON:0002227,UBERON:0002329,UBERON:0001846,UBERON:0001016,UBERON:0003128,UBERON:0000153,UBERON:0007811,UBERON:0002204,UBERON:0001434,UBERON:0000924,UBERON:0005743,UBERON:0004456,UBERON:0002241,UBERON:0002105,UBERON:0001678,UBERON:0003129,UBERON:0001694,UBERON:0004681,UBERON:0001839,UBERON:0001690,UBERON:0001844,UBERON:0001849,UBERON:0002499,UBERON:0005944,UBERON:0001855,UBERON:0001703,UBERON:0003077,UBERON:0009142,UBERON:0003069,UBERON:0003051,UBERON:0004288,UBERON:0004637,UBERON:0006601,UBERON:0006603,UBERON:0004761,UBERON:0010113,UBERON:0003089,UBERON:0003059,UBERON:0009123,UBERON:0007282,UBERON:0009618,UBERON:0007285,UBERON:0009617,UBERON:0005641
|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:0000003,CL:0000197,CL:0000540,CL:0000055,CL:0000047,CL:0000144,CL:0000723,CL:0000048,CL:0000548,CL:0000034,CL:0000012,CL:0002321,CL:0000063,CL:0000066,CL:0002371,CL:0002319,CL:0000221,CL:0000393,CL:0000006,CL:0002374,CL:0002491,CL:0000220,CL:0000004,CL:0000031,CL:0000211,CL:0000404,CL:0000255,CL:0000202,CL:0000199,CL:0000098,CL:0000855,CL:0000589,CL:0000133
|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_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
|comment=Previously: Math1- Inner ear hair cells - organ of corti, pool1
|created_by=
|created_by=

Revision as of 22:39, 4 July 2012


Name:Atoh+ Inner ear hair cells - organ of corti, pool1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueorgan of corti
dev stageNA
sexmixed
ageNA
cell typehair cell, organ of corti, inner
cell lineNA
companyNA
collaborationAlbert Edge (Department of Otolaryngology, Harvard Medical School)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs12533

00
10.073
100
1000.0645
10000
1001-0.0749
10020.246
1003-0.0306
10040
10050
10060.113
10070.246
10080
10090.168
101-0.0178
10100
10110.0288
10120
1013-0.00408
1014-0.0874
10150.239
10160.31
10170
10180
10190
1020
10200
10210
10220.0503
10230
10240
10250
10260
10270.237
10280
1029-0.176
103-0.0142
10300
10310.435
10320.203
10330.00678
10340
10350
10360.0695
10370.121
10380.047
10390.00983
1040
1040-0.0382
10410



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


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

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data
library id: CNhs12533This sample isn't target for the analysis

FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data
library id: CNhs12533This sample isn't target for the analysis

de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs12533


FANTOM5 (FF) ontology

Direct parent terms


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

CL: Cell type
0000000 (cell), 0000000 (cell)
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)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

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