Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2874

Putative Beta-glucosidase A (NCBI)

CircVis
Functional Annotations (8)
Function System
Beta-glucosidase/6-phospho-beta-glucosidase/beta-galactosidase cog/ cog
carbohydrate metabolic process go/ biological_process
beta-glucosidase activity go/ molecular_function
cation binding go/ molecular_function
Cyanoamino acid metabolism kegg/ kegg pathway
Starch and sucrose metabolism kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
BGL tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2874
(Mouseover regulator name to see its description)

RSP_2874 is regulated by 17 influences and regulates 0 modules.
Regulators for RSP_2874 (17)
Regulator Module Operator
RSP_1225 229 tf
RSP_1231 229 tf
RSP_1435 229 tf
RSP_1952 229 tf
RSP_2494 229 tf
RSP_2533 229 tf
RSP_2681 229 tf
RSP_2889 229 tf
RSP_3621 229 tf
RSP_0386 233 tf
RSP_1518 233 tf
RSP_1790 233 tf
RSP_2130 233 tf
RSP_2425 233 tf
RSP_2867 233 tf
RSP_3464 233 tf
RSP_3694 233 tf

Warning: RSP_2874 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
8176 2.00e-05 AAacaGAAGgTCaAaaGagat
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8177 1.40e-06 agTTGcGActCcgAcGAaACTG
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8184 2.10e-07 CtGCatCcGcgCA.CCaaA.G
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8185 4.50e-02 AcaGGCGGGGgAtGggAAGGGGT
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for RSP_2874

RSP_2874 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Beta-glucosidase/6-phospho-beta-glucosidase/beta-galactosidase cog/ cog
carbohydrate metabolic process go/ biological_process
beta-glucosidase activity go/ molecular_function
cation binding go/ molecular_function
Cyanoamino acid metabolism kegg/ kegg pathway
Starch and sucrose metabolism kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
BGL tigr/ tigrfam
Module neighborhood information for RSP_2874

RSP_2874 has total of 52 gene neighbors in modules 229, 233
Gene neighbors (52)
Gene Common Name Description Module membership
RSP_0116 RSP_0116 hypothetical protein (NCBI) 14, 229
RSP_0118 RSP_0118 Cytochrome c oxidase, subunit IIc (NCBI) 77, 229
RSP_0700 RSP_0700 probable glycosyltransferase (NCBI) 233, 326
RSP_0701 RSP_0701 ABC peptide transporter, fused ATPase domains (NCBI) 233, 326
RSP_1069 RSP_1069 hypothetical protein (NCBI) 233, 267
RSP_1370 RSP_1370 Alpha amylase, catalytic subdomain (NCBI) 124, 229
RSP_1392 thiP ABC thiamine transporter, inner membrane subunit (NCBI) 233, 234
RSP_1471 RSP_1471 hypothetical protein (NCBI) 140, 229
RSP_1638 RSP_1638 hypothetical protein (NCBI) 233, 236
RSP_1639 RSP_1639 hypothetical protein (NCBI) 233, 253
RSP_1640 RSP_1640 hypothetical protein (NCBI) 168, 233
RSP_1641 RSP_1641 hypothetical protein (NCBI) 233, 300
RSP_1644 RSP_1644 hypothetical protein (NCBI) 233, 300
RSP_1645 RSP_1645 putative phage-related protein (NCBI) 191, 233
RSP_1646 RSP_1646 possible transmembrane protein (NCBI) 233, 308
RSP_1694 RSP_1694 Probable short-chain dehydrogenase/reductase (NCBI) 233, 304
RSP_1782 RSP_1782 hypothetical membrane protein (NCBI) 233, 235
RSP_1783 RSP_1783 Predicted membrane protein (NCBI) 233, 235
RSP_1796 sodC Putative Copper/Zinc superoxide dismutase (NCBI) 150, 229
RSP_1822 RSP_1822 hypothetical protein (NCBI) 229, 238
RSP_1900 RSP_1900 hypothetical protein (NCBI) 91, 233
RSP_1951 RSP_1951 hypothetical protein (NCBI) 56, 229
RSP_1952 RSP_1952 Cold-shock DNA-binding domain protein (NCBI) 56, 229
RSP_2021 shp Mono-heme class I cytochrome c (NCBI) 150, 229
RSP_2022 RSP_2022 Cytochrome b/diheme cytochrome c hybrid protein (NCBI) 103, 229
RSP_2023 RSP_2023 hypothetical protein (NCBI) 229, 304
RSP_2024 cspA Cold shock protein cspA (NCBI) 56, 229
RSP_2219 RSP_2219 putative lipid A biosynthesis lauroyl acyltransferase (NCBI) 183, 229
RSP_2751 RSP_2751 hypothetical protein (NCBI) 105, 229
RSP_2807 RSP_2807 putative cytochrome b (NCBI) 14, 229
RSP_2808 RSP_2808 hypothetical protein (NCBI) 14, 229
RSP_2871 aglG ABC alpha-glucoside transporter, inner membrane subunit AglG (NCBI) 229, 235
RSP_2874 RSP_2874 Putative Beta-glucosidase A (NCBI) 229, 233
RSP_2884 glgX glycogen debranching enzyme (NCBI) 233, 340
RSP_2889 RSP_2889 Transcriptional regulator (NCBI) 185, 229
RSP_2890 RSP_2890 Copper-translocating P-type ATPase (NCBI) 185, 229
RSP_2891 RSP_2891 Putative copper chaperone (NCBI) 185, 229
RSP_2964 RSP_2964 hypothetical protein (NCBI) 229, 244
RSP_3122 RSP_3122 putative Glutathione S-transferase (NCBI) 233, 249
RSP_3287 upgC ABC glycerol-3-phosphate transporter, ATPase subunit UpgC (NCBI) 115, 233
RSP_3288 ugpE ABC glycerol-3-phosphate transporter, inner membrane subunit UgpE (NCBI) 115, 233
RSP_3289 ugpA ABC glycerol-3-phosphate transporter, inner membrane subunit UgpA (NCBI) 115, 233
RSP_3290 ugpB ABC glycerol-3-phosphate transporter, periplasmic binding protein, UgpB (NCBI) 115, 233
RSP_3543 RSP_3543 Probable type I restriction-modification system restriction subunit (NCBI) 191, 229
RSP_3621 RSP_3621 Cold-shock DNA-binding protein (NCBI) 56, 229
RSP_3622 RSP_3622 hypothetical protein (NCBI) 56, 229
RSP_3651 RSP_3651 putative membrane protein (NCBI) 189, 233
RSP_3652 RSP_3652 Predicted phage phi-C31 gp36 major capsid-like protein (NCBI) 141, 233
RSP_3653 RSP_3653 hypothetical protein (NCBI) 141, 233
RSP_3693 RSP_3693 BtpA protein (NCBI) 94, 233
RSP_3694 RSP_3694 Putative transcription activator (NCBI) 94, 233
RSP_3788 RSP_3788 hypothetical protein (NCBI) 77, 233
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for RSP_2874
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend