Complete list of species in the Network Portal database
Explore Network Org code Species Taxonomy id Genes Regulators STRING Data Data source Gene Expression Data
bce Bacillus cereus ATCC14579 226900 (NCBI) 5501 376 226900 Bacillus cereus ATCC14579 (Microbes Online) bce-ratios.tsv
bsu Bacillus subtilis 224308 (NCBI) 4313 319 224308 Bacillus subtilis (Microbes Online) bsu-ratios.tsv
bth Bacteroides thetaiotaomicron VPI-5482 226186 (NCBI) 4902 263 226186 Bacteroides thetaiotaomicron VPI-5482 (Microbes Online) bth-ratios.tsv
cje Campylobacter jejuni 192222 (NCBI) 1711 39 192222 Campylobacter jejuni (Microbes Online) cje-ratios.tsv
cac Clostridium acetobutylicum 272562 (NCBI) 3955 259 272562 Clostridium acetobutylicum (Microbes Online) cac-ratios.tsv
dvu Desulfovibrio vulgaris Hildenborough 882 (NCBI) 3661 128 882 Desulfovibrio vulgaris Hildenborough (Microbes Online) dvu-ratios.tsv
eco Escherichia coli K12 83333 (NCBI) 4497 310 83333 Escherichia coli K12 (Microbes Online) eco-ratios.tsv
Generic Generic -1 (NCBI) 0 0 -1 Generic (Microbes Online) Generic-ratios.tsv
gsu Geobacter sulfurreducens 243231 (NCBI) 3519 156 243231 Geobacter sulfurreducens (Microbes Online) gsu-ratios.tsv
hal Halobacterium salinarum NRC-1 64091 (NCBI) 2701 125 64091 Halobacterium salinarum NRC-1 (Microbes Online) hal-ratios.tsv
mmp Methanococcus maripaludis S2 267377 (NCBI) 1863 57 267377 Methanococcus maripaludis S2 (Microbes Online) mmp-ratios.tsv
mtu Mycobacterium tuberculosis H37Rv 83332 (NCBI) 0 0 83332 Mycobacterium tuberculosis H37Rv (Microbes Online) mtu-ratios.tsv
pae Pseudomonas aeruginosa 208964 (NCBI) 5646 475 208964 Pseudomonas aeruginosa (Microbes Online) pae-ratios.tsv
rsp Rhodobacter sphaeroides 2.4.1 272943 (NCBI) 4341 231 272943 Rhodobacter sphaeroides 2.4.1 (Microbes Online) rsp-ratios.tsv
syf Synechococcus elongatus PCC 7942 1140 (NCBI) 2717 90 1140 Synechococcus elongatus PCC 7942 (Microbes Online) syf-ratios.tsv
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Species List Help

We can build a regulatory network for any organism whose genome is sequenced if sufficient gene expression data are available. In order to show the flexibility of network portal, we built regulatory networks for organisms from different phylogenies and with varying genome complexity and available amounts of gene expression data.

The first release of Network Portal includes 2 Archaea and 11 Bacteria, including 3 Firmicutes, 6 Proteobacteria, a Cyanobacterium, and a Bacteroidetes species. These organisms include a number of well-studied model organisms as well as species that are of interest due to human pathogenicity, human symbiosis, biofuel production, or bioremediation activity. Comparative network analysis will benefit from the selection of species from distantly related clades, including representation from multiple phyla within Bacteria and multiple classes within Archaea, and from the selection of some closely related species, such as the two Bacillus sp.

The smallest genome in the Network Portal is that of C. jejuni with 1711 genes and the largest is P. aeruginosa with 5646 genes. The largest and smallest expression datasets are 1661 and 58 for H. salinarum and M. maripaludis, respectively. The Network Portal can rapidly be expanded to include the >100 organisms for which there is already sufficient gene expression data available in public databases for robust regulatory network inference.

Species List table shows organism for which we currently have network models available. Clicking on the Species name will take you the species specific page to acces all related resources. Taxonomy id shows link to taxonomy page at NCBI. Total number of genes in the genome as well as Number of regulators are also listed in the table and linked to table listing all the genes and regulators.

In order to access the available network model, click on the network icon ().