Difference between revisions of "XENLA GeneModel2012"
From Marcotte Lab
(→Orthologous genes) |
(→Orthologous genes) |
||
Line 38: | Line 38: | ||
= 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). | + | 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). |
+ | species_list = ['XENLA','HUMAN','XENTR','MOUSE','DANRE','CHICK','CAEEL','DROME'] | ||
+ | |||
+ | {| class="wikitable" | ||
+ | |- | ||
+ | ! scope="col"| | ||
+ | ! scope="col"| XENLA (''X. laevis'') | ||
+ | ! scope="col"| HUMAN | ||
+ | ! scope="col"| XENTR (''X. tropicalis'') | ||
+ | ! scope="col"| MOUSE | ||
+ | ! scope="col"| DANRE (zebrafish) | ||
+ | ! scope="col"| CHICK (chicken) | ||
+ | ! scope="col"| CAEEL (worm) | ||
+ | ! scope="col"| DROME (fly) | ||
+ | |- | ||
+ | ! scope="row"| Stage pep as query | ||
+ | |[[xdata:/J/blast/Taira201203_XENLA_stage_pep_final.XENLA_prot_v4.bp+_summary| Stage pep --> XENLA]] | ||
+ | |[[xdata:/J/blast/Taira201203_XENLA_stage_pep_final.HUMAN_ens66_pep_longest.bp+_summary| Stage pep --> HUMAN]] | ||
+ | |[[xdata:/J/blast/Taira201203_XENLA_stage_pep_final.XENTR_ens66_pep_longest.bp+_summary| Stage pep --> XENTR]] | ||
+ | |[[xdata:/J/blast/Taira201203_XENLA_stage_pep_final.MOUSE_ens66_pep_longest.bp+_summary| Stage pep --> MOUSE]] | ||
+ | |[[xdata:/J/blast/Taira201203_XENLA_stage_pep_final.DANRE_ens66_pep_longest.bp+_summary| Stage pep --> DANRE]] | ||
+ | |[[xdata:/J/blast/Taira201203_XENLA_stage_pep_final.CHICK_ens66_pep_longest.bp+_summary| Stage pep --> CHICK]] | ||
+ | |[[xdata:/J/blast/Taira201203_XENLA_stage_pep_final.CAEEL_ens66_pep_longest.bp+_summary| Stage pep --> CAEEL]] | ||
+ | |[[xdata:/J/blast/Taira201203_XENLA_stage_pep_final.DROME_ens66_pep_longest.bp+_summary| Stage pep --> DROME]] | ||
+ | |- | ||
+ | ! scope="row"| Stage pep as target | ||
+ | |[[xdata:/J/blast/XENLA_prot_v4.Taira201203_XENLA_stage_pep_final.bp+_summary| Stage pep --> XENLA]] | ||
+ | |[[xdata:/J/blast/HUMAN_ens66_pep_longest.Taira201203_XENLA_stage_pep_final.bp+_summary| HUMAN --> Stage pep]] | ||
+ | |[[xdata:/J/blast/XENTR_ens66_pep_longest.Taira201203_XENLA_stage_pep_final.bp+_summary| XENTR --> Stage pep]] | ||
+ | |[[xdata:/J/blast/MOUSE_ens66_pep_longest.Taira201203_XENLA_stage_pep_final.bp+_summary| MOUSE --> Stage pep]] | ||
+ | |[[xdata:/J/blast/DANRE_ens66_pep_longest.Taira201203_XENLA_stage_pep_final.bp+_summary| DANRE --> Stage pep]] | ||
+ | |[[xdata:/J/blast/CHICK_ens66_pep_longest.Taira201203_XENLA_stage_pep_final.bp+_summary| CHICK --> Stage pep]] | ||
+ | |[[xdata:/J/blast/CAEEL_ens66_pep_longest.Taira201203_XENLA_stage_pep_final.bp+_summary| CAEEL --> Stage pep]] | ||
+ | |[[xdata:/J/blast/DROME_ens66_pep_longest.Taira201203_XENLA_stage_pep_final.bp+_summary| DROME --> Stage pep]] | ||
+ | |- | ||
+ | ! scope="row"| Tissue pep as query | ||
+ | |[[xdata:/J/blast/Taira201203_XENLA_tissue_pep_final.XENLA_prot_v4.bp+_summary| Tissue pep --> XENLA]] | ||
+ | |[[xdata:/J/blast/Taira201203_XENLA_tissue_pep_final.HUMAN_ens66_pep_longest.bp+_summary| Tissue pep --> HUMAN]] | ||
+ | |[[xdata:/J/blast/Taira201203_XENLA_tissue_pep_final.XENTR_ens66_pep_longest.bp+_summary| Tissue pep --> XENTR]] | ||
+ | |[[xdata:/J/blast/Taira201203_XENLA_tissue_pep_final.MOUSE_ens66_pep_longest.bp+_summary| Tissue pep --> MOUSE]] | ||
+ | |[[xdata:/J/blast/Taira201203_XENLA_tissue_pep_final.DANRE_ens66_pep_longest.bp+_summary| Tissue pep --> DANRE]] | ||
+ | |[[xdata:/J/blast/Taira201203_XENLA_tissue_pep_final.CHICK_ens66_pep_longest.bp+_summary| Tissue pep --> CHICK]] | ||
+ | |[[xdata:/J/blast/Taira201203_XENLA_tissue_pep_final.CAEEL_ens66_pep_longest.bp+_summary| Tissue pep --> CAEEL]] | ||
+ | |[[xdata:/J/blast/Taira201203_XENLA_tissue_pep_final.DROME_ens66_pep_longest.bp+_summary| Tissue pep --> DROME]] | ||
+ | |- | ||
+ | ! scope="row"| Tissue pep as target | ||
+ | |[[xdata:/J/blast/XENLA_prot_v4.Taira201203_XENLA_tissue_pep_final.bp+_summary| Tissue pep --> XENLA]] | ||
+ | |[[xdata:/J/blast/HUMAN_ens66_pep_longest.Taira201203_XENLA_tissue_pep_final.bp+_summary| HUMAN --> Tissue pep]] | ||
+ | |[[xdata:/J/blast/XENTR_ens66_pep_longest.Taira201203_XENLA_tissue_pep_final.bp+_summary| XENTR --> Tissue pep]] | ||
+ | |[[xdata:/J/blast/MOUSE_ens66_pep_longest.Taira201203_XENLA_tissue_pep_final.bp+_summary| MOUSE --> Tissue pep]] | ||
+ | |[[xdata:/J/blast/DANRE_ens66_pep_longest.Taira201203_XENLA_tissue_pep_final.bp+_summary| DANRE --> Tissue pep]] | ||
+ | |[[xdata:/J/blast/CHICK_ens66_pep_longest.Taira201203_XENLA_tissue_pep_final.bp+_summary| CHICK --> Tissue pep]] | ||
+ | |[[xdata:/J/blast/CAEEL_ens66_pep_longest.Taira201203_XENLA_tissue_pep_final.bp+_summary| CAEEL --> 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]], | * 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]], |
Revision as of 13:52, 3 August 2012
Contents |
Data summary
Disclaimer
|
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
- From tissue samples: Protein FASTA cDNA FASTA
- From stage samples: Protein FASTA cDNA FASTA
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). species_list = ['XENLA','HUMAN','XENTR','MOUSE','DANRE','CHICK','CAEEL','DROME']
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
- Affymetrix microarray v.1 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL1318)
- Affymetrix microarray v.2 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL10756)
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)
- Edward M. Marcotte (University of Texas at Austin)
- John B. Wallingford (University of Texas at Austin)
- Taejoon Kwon (University of Texas at Austin)
- Texas Advanced Computing Center (TACC)