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 Collaborative data area:
This page contains some of the on-going and/or published projects that the CBRG have produced in collaboration
with members of the Medical Sciences Division at Oxford University.
It is intended that these pages will provide a valuable data resource for CBRG account holders as well
as the wider scientific community.
BioPivot: Mining Biological Data using Microsoft Live Labs' Pivot Viewer
Description:
Easy to use but powerful data querying and visualization tools to aid analysis of next generation sequencing are required to understand the large amount of data generated. BioPivot is a suite of tools for building Microsoft Live Labs Pivot collections. This allows the user to visualize, query and filter many thousands of
genome regions containing ChIP-Seq peaks, or any experiment where it is desirable to rapidly view and query a large number of genome regions.
Installation and usage instructions are here.
Photo-Induced Site-Selective Protein Cleavage
Description:
1. Multiple sequence alignments
- Archaic, bacterial and eukaryotic GH1 proteins: Jalview jar file | fasta alignment |
- Archaea GH1 proteins:
Jalview jar file | fasta alignment
- Bacteria GH1 proteins:
Jalview jar file | fasta alignment
- Eukaryota GH1 proteins:
Jalview jar file | fasta alignment
- Archaic, bacterial and eukaryotic GH1 proteins and additional proteins found by HMM searching Genpept: jar file | fasta alignment
2. MEME Analysis
GH1 proteins analysed by MEME showing the conserved His motif in Motif 2.
3. Phylogenetic Analysis
- Archaic, bacterial and eukaryotic GH1 proteins: tree file
- Archaea GH1 proteins: tree file
- Bacteria GH1 proteins:tree file
- Eukaryota GH1 proteins:tree file
- Archaic, bacterial and eukaryotic GH1 proteins and additional proteins found by HMM searching Genpept: tree file
Reference:Photo-Induced, Family-Specific, Site-Selective Cleavage of TIM-barrel Proteins (Submitted)
Floyd, N.; Oldham, N. J.; Eyles, C. J.; Taylor, S.; Filatov, D. A.; Brouard, M.; Davis, B. G., Journal of the American Chemical Society, Submitted
It is recommended that alignments are viewed in Jalview and tree files in Dendroscope.
See the paper for details on construction of alignments and trees.
MIAA - Minimum Information about Anatomy
Description: MIAA is a controlled vocabulary whose terms and IDs can be used to annotate tissue-associated data.
MIAA is in obo format and can be read in the Oboedit and COBrA browsers.
The controlled vocabulary contains about 400 tissue and timeline terms that cover all the major taxa. All terms are annotated with the IDs and synonyms of any equivalent term in the 20 or
so anatomy ontologies included on the OBO site.
Download a more detailed introduction and some screenshots. 
Download the MIAA obo format file.
Reference: (in preparation).
Mouse Immunorray
Description: These pages provide background information for a mouse oligonucleotide-based
microarray containing probes for a targeted set of immune-related genes. As well
as providing information on possible false-positive hybridizations to facilitate proper validation of experimental observations,
it also provides links to the target genes for each of the probes on the array.
Reference: Description of a microarray targeted to genes important in mouse immune responses and
differentiation. (in preparation).
Differential gene expression analysis
Description: Differential gene expression analysis using cDNA libraries has been improved by
the introduction of an accurate method of assigning ESTs to genes and a novel maximum likelihood statistical scoring of differential
gene expression between two pools of cDNA libraries. A web tool employing these methods has been developed so that researchers can
design their own differential gene expression experiments.
As far as possible, each Human EST from all of the cDNA libraries at GenBank
has been assigned to a RefSeq gene or gene prediction based on the new Jake cluster algorithm so that any tissue of interest can be queried provided
cDNA libraries exist. The interface is similar to the SAGEmap
xProfiler tool where the user selects a pool of cDNA libraries in group A and compares with it a pool chosen in group B. The results
are returned to the user as a table, reporting the q-value and whether the gene is up or down regulated in pool A.
Authors: John Herbert and Dov Stekel
Visualisation of quantitative biological data on genomes using Apollo
As part of his Bioinformatics MSc project at Oxford University, Salman
Sheikh (supervised by the CBRG) has developed an extension to Apollo
that allows histogram data to be uploaded and visualised.
Bacterial Pathogenesis and Functional Genomics Group
This section provides background information and data supporting the work of the Saunders
group at the Sir William Dunn School of Pathology.
Arp - this data is background information for: "The function and structure of the alanine-binding (LRP-family)
response regulator of Neisseria controlling metabolic responses to oxygen limitation." - Capper et al (in preparation).
- FA1090-arp GBrowse database - (Note: password required)
- MC58-arp GBrowse database - (Note: password required)
Artefactual microarray probe signals - Microarray probes generating artefactual signals using dendrimer 3DNA900 labeling - this data
is supporting information for: "Differences in transcriptional properties determine the replication and
experimental conditions required for transcriptional profiling in different species." - Capper et al (in preparation)
Lists of probes exhibiting false dendrimer labelling:
- E. coli (- ArrayExpress accession number: A-MEXP-841)
- B. subtilis (- ArrayExpress accession number: A-MEXP-839)
- A. thaliana (- ArrayExpress accession: A-MEXP-950)
Iron and Iron donors - this data is background information for: "Host Iron Binding Proteins acting as Niche Indicators in
Neisseria meningitidis" - Jordan and Saunders (in preparation).
- MC58 iron GBrowse database - (Note: password required)
AsnC - GBrowse database showing expression profiles described in Ren et al
(J. Biol. Chem. 2007 Mar 20) "The
structure and transcriptional analysis of a global regulator from Neisseria meningitidis".
- AsnC GBrowse database
FNR and NarQ-NarP - GBrowse database showing expression profiles described in Whitehead et al
(BMC
Genomics 2007 8: 35) "The small FNR regulon of Neisseria
gonorrhoeae: comparison with the larger E. coli FNR regulon and interaction with the NarQ-NarP regulon".
- FNR and NarQ-NarP GBrowse database
NarPQ - GBrowse database showing expression profiles described in, Overton et al (J.
Biol. Chem., 281, 33115-33126, 2006) "Coordinated regulation of the Neisseria
gonorrhoeae truncated denitrification pathway by the nitric oxide-sensitive repressor NsrR, and nitrite-insensitive
NarQ-NarP".
- NarPQ GBrowse database
Comparative genome analyses - Neisserial comparative genome analysis vs N. lactamica. This data is
additional information for: Snyder and Saunders: "The majority of genes in
the pathogenic Neisseria species are present in non-pathogenic Neisseria lactamica, including those designated as virulence
genes" BMC Genomics 2006, 7:128, in which the genes detected in N. lactamica are indicated relative to the complete genomes of
N. gonorrhoeae strain FA1090 and N. meningitidis strains MC58 and Z2491.
- NLA CGH FA1090 - N. gonorrhoeae strain FA1090
- NLA CGH MC58 - N. meningitidis serogroup B strain MC58
- NLA CGH Z2491 - N. meningitidis serogroup A strain Z2491
Annotation comparison - GBrowse database showing the official NGO annotation submitted
with AE004969 for N. gonorrhoeae strain FA1090 with the XNG
annotation used for the generation of the pan-Neisseria microarray, also showing the annotations for the similar genes annotated in N. meningitidis
stains MC58 (NMB) and Z2491 (NMA)
- strain FA1090 - N. gonorrhoeae strain FA1090
marR - this data is background information for: "Neisserial MarR: A pathogen-specific regulator with species-specific
regulatory activities." - Nichols et al (in preparation).
- N. gonorrhoeae strain FA1090 - (Note: password required)
- N. meningitidis serogroup B strain MC58 - (Note: password required)
Temperature response - this data is background information for: "Differing 'fever' responses in N. meningitidis and
N. gonorrhoeae leading to reduced expression of surface proteins likely to be immunological targets" - Ahmat, Snyder and Saunders (in preparation).
- N. gonorrhoeae strain FA1090 - (Note: password required)
- N. meningitidis serogroup B strain MC58 - (Note: password required)
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