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This site presents data integration, analysis and management environment for systems biology research for studying host-pathogen interaction.
We developed methods and tools for simplifying and streamlining the process of integration of diverse experimental data types,
including molecular interaction, gene expression levels, genomic sequences, protein structure information, phylogenetic classification,
and virulence data for pathogen-related studies.
Systems level studies on Influenza virus and Streptococcus pneumoniae identified host molecular pathways that appear to be
induced or repressed during infection, and these results highlight pathways exhibiting responses specific for a given pathogen infection.
The results demonstrate the usefulness of dynamic data integration techniques, and enable a hypothesis generation platform for major human
disease systems. In this integrated database we provide access to heterogeneous information that are of value to researchers in epidemiology,
virology and vaccine development.
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| Current DB content (Influenza part) |
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| Genomes: |
22949 |
| Countries: |
113 |
| Locations: |
1605 |
| Host organisms: |
354 |
| Isolation sources: |
22949 |
| Protein sequences: |
99117 |
| Nucleotide sequences: |
79431 |
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Cumulative Number of Confirmed Human Cases of Influenza A/(H5N1) Reported to WHO
| Country |
2003 |
2004 |
2005 |
2006 |
2007 |
2008 |
2009 |
Total |
| cases | deaths |
cases | deaths |
cases | deaths |
cases | deaths |
cases | deaths |
cases | deaths |
cases | deaths |
cases | deaths |
| Azerbaijan |
0 | 0 | 0 |
0 | 0 | 0 |
8 | 5 | 0 |
0 | 0 | 0 |
0 | 0 | 8 |
5 |
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| Bangladesh |
0 | 0 | 0 |
0 | 0 | 0 |
0 | 0 | 0 |
0 | 1 | 0 |
0 | 0 | 1 |
0 |
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| Cambodia |
0 | 0 | 0 |
0 | 4 | 4 |
2 | 2 | 1 |
1 | 1 | 0 |
0 | 0 | 8 |
7 |
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| China |
1 | 1 | 0 |
0 | 8 | 5 |
13 | 8 | 5 |
3 | 4 | 4 |
7 | 4 | 38 |
25 |
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| Djibouti |
0 | 0 | 0 |
0 | 0 | 0 |
1 | 0 | 0 |
0 | 0 | 0 |
0 | 0 | 1 |
0 |
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| Egypt |
0 | 0 | 0 |
0 | 0 | 0 |
18 | 10 | 25 |
9 | 8 | 4 |
36 | 4 | 87 |
27 |
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| Indonesia | 0 | 0 | 0 | 0 | 20 | 13 | 55 | 45 | 42 | 37 |
24 | 20 | 0 | 0 | 141 |
115 |
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| Iraq | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 2 |
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| Lao People's Democratic Republic | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 2 | 0 | 0 | 0 | 0 | 2 | 2 |
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| Myanmar | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
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| Nigeria | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 1 | 1 |
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| Pakistan | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 1 | 0 | 0 | 0 | 0 | 3 | 1 |
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| Thailand | 0 | 0 | 17 | 12 | 5 | 2 | 3 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 25 | 17 |
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| Turkey | 0 | 0 | 0 | 0 | 0 | 0 | 12 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 12 | 4 |
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| Viet Nam | 3 | 3 | 29 | 20 | 61 | 19 | 0 | 0 | 8 | 5 | 6 | 5 | 4 | 4 | 111 | 56 |
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| Total | 4 | 4 | 46 | 32 | 98 | 43 | 115 | 79 | 88 | 59 |
44 | 33 | 47 | 12 |
442 |
262 |
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Database statistics
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Category
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Number of entities
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Examples
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Relations
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197 616 248
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Co-citation, co-expression
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Physical interactions
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56 882 654
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Protein-protein, protein-DNA, ligand-protein, ...
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Small molecules
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9 957 879
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Chemical molecules, ligands, compounds, glycans
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Proteins
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5 647 773
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p53, NF-kappaB
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Publications
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3 189 964
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PubMed
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Interactions
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2 750 297
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Genetic interactions
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Genes
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2 546 676
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TP53
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Orthology groups
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2 143 144
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COGs
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Sets
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2 115 885
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Biochemical reactions
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1 715 618
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Photosynthesis, respiration
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Run of genes
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372 937
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Operon
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Organisms
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334 230
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Homo sapiens
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Pathways
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150 582
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KEGG
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Experiments
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45 125
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Proteomics experiments
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Protein molecular functions
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8 570
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protein kinase
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Microarray experiments
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5 971
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NCBI GEO experiments
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Cells
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1 341
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Pyramidal neurons
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Grouping
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1 011
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Homology clusters
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Other physical entities
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831
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Regulatory regions, promoters
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Enzymes
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766
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glyoxalase I
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Classes
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47
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gene, protein, regulatory region
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Collections
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26
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Functional categories
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25
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Families, PFAM protein classification
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Integrated databases
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104
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BIND, TRANSFAC
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