Personal tools

FF:12158-128G7

From FANTOM5_SSTAR

Jump to: navigation, search


Name:Atoh+ Inner ear hair cells - organ of corti, pool1
Species:Mouse (Mus musculus)
Library ID:CNhs12533
Sample type:primary cells
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
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

Accession numbers
MethodSample accession id
CAGE  SAMD00005207
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12533 CAGE DRX008761 DRR009633
Accession ID Mm9

Library idBAMCTSS
CNhs12533 DRZ001058 DRZ002443
Accession ID Mm10

Library idBAMCTSS
CNhs12533 DRZ012408 DRZ013793
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)


Transcription factors with enriched expression in this sample
Ranked 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 sample
Ranked 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

MCL coexpression id Coexpression dpi cluster scores median value
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 sample
Summary: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 motifs
Summary: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: CNhs12533This sample isn't target for the analysis

FANTOM5 phase1 novel unique motifs
Summary: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: CNhs12533This sample isn't target for the analysis

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

library id: CNhs12533


FANTOM5 (FF) ontology


Direct parent terms


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)
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)