| Links |
| PUBLICATIONS related to this work ( please quote! ) |
|
|
BMC Bioinformatics (2010): "GATExplorer: genomic and transcriptomic explorer; mapping expression probes
to gene loci, transcripts, exons and ncRNAs". Risueño A, Fontanillo C, Dinger ME, De Las Rivas J.
BMC Bioinformatics (2010) 11:221. PMID: 20429936.
|
|
| PLoS ONE (2008):
"Human gene coexpression landscape: confident network derived from tissue transcriptomic profiles".
Prieto C, Risueño A, Fontanillo C, De Las Rivas J.
PLoS One (2008) 3(12):e3911. PMID: 19081792.
|
| Technologies |
| PHP: Hypertext
Pre-processor |
| Ming:
Library for generating Macromedia Flash files (.swf) |
| MySQL:
Relational database server. |
| Apache: Web
application server |
| Fedora:
Linux operating system |
| BLAST: Basic Local Alignment and Search Tool |
| Java: Java
programming platform |
| R:
language and environment for statistical computing and graphics |
| BioConductor:
source and open development software project for the analysis and comprehension of genomic data |
| Databases |
| Ensembl:
Browser and large data source for eukaryotic genomes with many integrated information |
| RNAdb:
RNA database including many ncRNAs derived from large ESTs studies |
| Affymetrix:
Manufacturer of DNA microarrays |
| Gene Atlas:
Gene Expression Atlas Project |
| Other Related References |
| References related to probe mapping: |
• Gautier et al. (2004). PMID:
15310390
Alternative mapping of probes to genes for Affymetrix chips. |
• Mecham et al. (2004). PMID:
15161944
Sequence-matched probes produce increased cross-platform consistency and more
reproducible biological results in microarray-based gene expression measurements. |
• Harbig et al. (2005). PMID:
15722477
A sequence-based identification of the genes detected by probesets
on the Affymetrix U133 plus 2.0 array. |
• Zhang et al. (2005). PMID:
15718097
Detecting false expression signals in high-density oligonucleotide arrays
by an in silico approach. |
• Leong et al. (2005). PMID:
15746287
ADAPT: a database of affymetrix probesets and transcripts. |
• Carter et al. (2005). PMID:
15850491
Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray
probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. |
• Dai et al. (2005). PMID:
16284200
Evolving gene/transcript definitions significantly alter the
interpretation of GeneChip data. |
• Sandberg and Larsson (2007). PMID:
17288599
Improved precision and accuracy for microarrays using updated probe set definitions. |
• Lu et al. (2007). PMID:
17394657
Transcript-based redefinition of grouped oligonucleotide probe sets using AceView:
high-resolution annotation for microarrays. |
• Liu et al. (2007). PMID:
17660211
AffyProbeMiner: a web resource for computing or retrieving accurately
redefined Affymetrix probe sets. |
• Hijikata et al. (2007). PMID:
17893089
Construction of an open-access database that integrates cross-reference
information from the transcriptome and proteome of immune cells. |
• Ferrari et al. (2007). PMID:
18005434
Novel definition files for human GeneChips based on GeneAnnot. |
| References related to gene expression profiling in different tissues: |
• Su et al. (2004). PMID:
15075390
A gene atlas of the mouse and human protein-encoding transcriptomes. |
• Liang et al. (2006). PMID:
16684803
Detecting and profiling tissue-selective genes. |
• Roth et al. (2006). PMID:
16572319
Gene expression analyses reveal molecular relationships among 20 regions
of the human CNS. |
