Difference between revisions of "XENLA GeneModel2012"

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(Orthologous genes)
(Orthologous genes)
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= Annotation =
 
= Annotation =
 
== Orthologous genes ==
 
== Orthologous genes ==
We used EnsEMBL-66 as main protein sequences. For ''X. laevis'', we used protein sequences from XenBase (downloaded on Dec-2011). These are top-3 genes (based on E-value), with > 40% aligned length (based on query sequence).  
+
We used EnsEMBL-66 as main protein sequences. For ''X. laevis'', we used protein sequences from XenBase (downloaded on Dec-2011). These are top-3 genes (based on E-value), with > 40% aligned length (based on query sequence). It should be mentioned that this is based on simple BLASTP search. We are currently working on more accurate orthology analysis based on phylgenetic tree based method.
species_list = ['XENLA','HUMAN','XENTR','MOUSE','DANRE','CHICK','CAEEL','DROME']
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{| class="wikitable"
 
{| class="wikitable"
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|[[xdata:/J/blast/DROME_ens66_pep_longest.Taira201203_XENLA_tissue_pep_final.bp+_summary| DROME --> Tissue pep]]
 
|[[xdata:/J/blast/DROME_ens66_pep_longest.Taira201203_XENLA_tissue_pep_final.bp+_summary| DROME --> Tissue pep]]
 
|}
 
|}
 
* Human: [[xdata:/J/blast/Taira201203_XENLA_stage_pep_final.HUMAN_ens66_pep_longest.bp+_summary| Stage_pep --> Human]] / [[xdata:/J/blast/HUMAN_ens66_pep_longest.Taira201203_XENLA_stage_pep_final.bp+_summary| Human --> Stage_pep]] / [[xdata:/J/blast/Taira201203_XENLA_tissue_pep_final.HUMAN_ens66_pep_longest.bp+_summary| Tissue_pep --> Human]] / [[xdata:/J/blast/HUMAN_ens66_pep_longest.Taira201203_XENLA_tissue_pep_final.bp+_summary| Human --> Tissue_pep]],
 
  
 
== Micriarray ==
 
== Micriarray ==

Revision as of 13:54, 3 August 2012

Contents

Data summary

Disclaimer

  • Data users may freely download and analyze sequences posted here.
  • Data users may use data to analyze their own data, i.e. reference database for MS/MS proteomics data, and/or RNA-seq data.
  • The publication and presentation of global analysis of data with these sequences are not allowed until 'data owner' (Dr. Masanori Taira) published the paper. As soon as the paper is accepted, we will post that info on this website.
  • If you have more question about this data, please contact Dr. Masanori Taira, Dr. Edward Marcotte, or Dr. Taejoon Kwon.

Taira201203_XENLA_tissue

Collect total RNA from14 Tissue of Xenopus laevis J strain.

  • Brain, eye, heart, intestine, kidney, liver, lung, muscle, ovary, pancreas, skin, spleen, stomach, testis
  • Sons & daughters of single pair of frogs (Their mother frog was used for 1st BAC-end sequencing)
  • Standard Illumina sample prep. (poly-A capture)
  • Illumina HiSeq 2000, 2x100 bp
  • 108.5 billions of nucleotide calls in total.
  • 55M ~ 130M reads/tissue (27M ~ 65M pairs)
  • Brief report for data processing

Taira201203_XENLA_stage

Collect total RNA from 11 different developmental stages of Xenopus laevis J strain embryo.

  • Stage 01, 08, 09, 10.5, 12, 15, 20, 25, 30, 35, 40
  • Sons & daughters of single pair of frogs (their mother frog was used for 1st BAC-end sequencing)
  • Standard Illumina sample prep. (poly-A capture)
  • Illumina HiSeq 2000, 2x100 bp
  • 163.8 billions of nucleotide calls in total.
  • 40M ~ 110M reads/tissue (20M ~ 55M pairs)
  • Brief report for data processing

Assembled transcripts

Raw sequences

Annotation

Orthologous genes

We used EnsEMBL-66 as main protein sequences. For X. laevis, we used protein sequences from XenBase (downloaded on Dec-2011). These are top-3 genes (based on E-value), with > 40% aligned length (based on query sequence). It should be mentioned that this is based on simple BLASTP search. We are currently working on more accurate orthology analysis based on phylgenetic tree based method.

XENLA (X. laevis) HUMAN XENTR (X. tropicalis) MOUSE DANRE (zebrafish) CHICK (chicken) CAEEL (worm) DROME (fly)
Stage pep as query Stage pep --> XENLA Stage pep --> HUMAN Stage pep --> XENTR Stage pep --> MOUSE Stage pep --> DANRE Stage pep --> CHICK Stage pep --> CAEEL Stage pep --> DROME
Stage pep as target Stage pep --> XENLA HUMAN --> Stage pep XENTR --> Stage pep MOUSE --> Stage pep DANRE --> Stage pep CHICK --> Stage pep CAEEL --> Stage pep DROME --> Stage pep
Tissue pep as query Tissue pep --> XENLA Tissue pep --> HUMAN Tissue pep --> XENTR Tissue pep --> MOUSE Tissue pep --> DANRE Tissue pep --> CHICK Tissue pep --> CAEEL Tissue pep --> DROME
Tissue pep as target Tissue pep --> XENLA HUMAN --> Tissue pep XENTR --> Tissue pep MOUSE --> Tissue pep DANRE --> Tissue pep CHICK --> Tissue pep CAEEL --> Tissue pep DROME --> Tissue pep

Micriarray

Contributors

  • Masanori Taira (Graduate School of Science, University of Tokyo)
  • Shuji Takahashi (Komaba Organization for Educational Excellence, College of Arts and Sciences, University of Tokyo)
  • Toshiaki Tanaka (Tokyo Institute of Technology)
  • Atsushi Toyoda and Asao Fujiyama (National Institute of Genetics)
  • Yutaka Suzuki (Graduate School of Frontier Sciences, University of Tokyo)