Personal tools

FF:11651-122E4: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 6: Line 6:
|created_by=
|created_by=
|creation_date=
|creation_date=
|datafreeze_phase=1
|def=
|def=
|fonse_cell_line=
|fonse_cell_line=

Revision as of 19:50, 29 June 2012


Name:Schwann, donor3
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueperipheral nervous system
dev stageNA
sexNA
ageNA
cell typeschwann cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberlot:3915
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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

CNhs12115



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: CNhs12115This 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: CNhs12115This 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: CNhs12115


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)
0000003 (native cell)
0000333 (migratory neural crest cell)
0000055 (non-terminally differentiated cell)
0000548 (animal cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002319 (neural cell)
0000221 (ectodermal cell)
0000095 (neuron associated cell)
0000243 (glial cell (sensu Vertebrata))
0000219 (motile cell)
0000325 (stuff accumulating cell)
0000215 (barrier cell)
0000630 (supportive cell)
0000217 (insulating cell)
0000328 (myelin accumulating cell)
0002573 (Schwann cell)
0000123 (neuron associated cell (sensu Vertebrata))
0000125 (glial cell)
0000030 (glioblast)
0000255 (eukaryotic cell)
0002376 (non-myelinating Schwann cell)
0000218 (myelinating Schwann cell;;Schwann cell)
0000692 (terminal Schwann cell)
0002377 (immature Schwann cell)
0000133 (neurectodermal cell)
0000339 (glioblast (sensu Vertebrata))
0002375 (Schwann cell precursor)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0000479 (tissue)
0000073 (regional part of nervous system)
0004121 (ectoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0005291 (embryonic tissue)
0006598 (presumptive structure)
0002532 (epiblast (generic))
0000010 (peripheral nervous system)
0001016 (nervous system)
0000924 (ectoderm)
0006601 (presumptive ectoderm)

FF: FANTOM5
NA

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