Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2835 ispD

Probable 4-diphosphocytidyl-2C-methyl-D-erythritol synthase (YgbP) (NCBI)

CircVis
Functional Annotations (7)
Function System
4-diphosphocytidyl-2-methyl-D-erithritol synthase cog/ cog
isoprenoid biosynthetic process go/ biological_process
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity go/ molecular_function
Terpenoid backbone biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
ispD tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2835
(Mouseover regulator name to see its description)

RSP_2835 is regulated by 21 influences and regulates 0 modules.
Regulators for RSP_2835 ispD (21)
Regulator Module Operator
RSP_0087 100 tf
RSP_0282 100 tf
RSP_0489 100 tf
RSP_0601 100 tf
RSP_1590 100 tf
RSP_2171 100 tf
RSP_2410 100 tf
RSP_2572 100 tf
RSP_2606 100 tf
RSP_2800 100 tf
RSP_2838 100 tf
RSP_2888 100 tf
RSP_2939 100 tf
RSP_2963 100 tf
RSP_3238 100 tf
RSP_3322 100 tf
RSP_1231 85 tf
RSP_2606 85 tf
RSP_2888 85 tf
RSP_2963 85 tf
RSP_3238 85 tf

Warning: RSP_2835 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
7890 5.80e+00 gAaactTCCaa
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7891 4.80e+02 AAAAGgGcgct
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7920 1.40e-01 GccTCGCcCAAggAacGgGCa
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7921 3.60e-02 GccGgctttccCgatgCGCacAgG
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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_2835

RSP_2835 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
4-diphosphocytidyl-2-methyl-D-erithritol synthase cog/ cog
isoprenoid biosynthetic process go/ biological_process
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity go/ molecular_function
Terpenoid backbone biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
ispD tigr/ tigrfam
Module neighborhood information for RSP_2835

RSP_2835 has total of 37 gene neighbors in modules 85, 100
Gene neighbors (37)
Gene Common Name Description Module membership
RSP_0162 RSP_0162 hypothetical protein (NCBI) 100, 118
RSP_0308 ureB Urease, beta subunit (NCBI) 16, 100
RSP_0309 ureA Urease, gamma subunit (NCBI) 16, 100
RSP_0310 ureD Urease accessory protein UreD (NCBI) 16, 100
RSP_0311 RSP_0311 Putative aminotransferase protein (NCBI) 16, 100
RSP_0312 RSP_0312 Aminotransferase class-III (NCBI) 16, 100
RSP_0590 RSP_0590 hypothetical protein (NCBI) 85, 382
RSP_0823 SHMT serine hydroxymethyltransferase protein (NCBI) 71, 85
RSP_0880 dadA putative oxidoreductase, possibly D-amino acid oxidase protein (NCBI) 85, 100
RSP_1134 Dxs 1 deoxyxylulose-5-phosphate synthase (NCBI) 100, 108
RSP_1135 ispA geranylgeranyl pyrophosphate synthetase (NCBI) 100, 108
RSP_1136 xseB exonuclease VII small subunit (NCBI) 100, 108
RSP_1175 ubiG 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4 benzoquinol methylase (NCBI) 85, 108
RSP_1338 ubiE methyltransferase (NCBI) 85, 108
RSP_1351 serC phosphoserine aminotransferase (NCBI) 85, 360
RSP_1352 RSP_1352 D-3-phosphoglycerate dehydrogenase (NCBI) 85, 360
RSP_1513 trpB Putative Tryptophan synthase beta chain (NCBI) 85, 382
RSP_1665 RSP_1665 putative RhtB family transporter (NCBI) 81, 85
RSP_1666 LytB 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (NCBI) 81, 85
RSP_2045 RSP_2045 hypothetical protein (NCBI) 100, 118
RSP_2047 RSP_2047 ThiF family protein (NCBI) 100, 358
RSP_2048 RSP_2048 hypothetical protein (NCBI) 100, 358
RSP_2249 RSP_2249 multidrug (Tetracycline) efflux pump, Major facilitator superfamily (MFS) (NCBI) 100, 108
RSP_2313 RSP_2313 D-isomer specific 2-hydroxyacid dehydrogenase (NCBI) 85, 118
RSP_2551 exoO Glycosyl transferase, family 2 (NCBI) 10, 100
RSP_2709 dxr probable 1-deoxy-D-xylulose 5-phosphate reductoisomerase protein (NCBI) 36, 100
RSP_2833 cinA Putative competence-damaged inducible protein (NCBI) 100, 318
RSP_2834 pgpA Putative Phosphatidylglycerophosphatase A (NCBI) 100, 318
RSP_2835 ispD Probable 4-diphosphocytidyl-2C-methyl-D-erythritol synthase (YgbP) (NCBI) 85, 100
RSP_2848 hemB Delta-aminolevulinic acid dehydratase (Porphobilinogen synthase) (NCBI) 85, 382
RSP_2963 RSP_2963 transcriptional regulator, Crp-Fnr family (NCBI) 85, 139
RSP_3207 RSP_3207 putative cobalamin biosynthesis protein CbiM (NCBI) 16, 100
RSP_3208 RSP_3208 putative CbiL protein (NCBI) 16, 100
RSP_3209 cbiQ ABC cobalt transporter, inner membrane subunit, CbiQ (NCBI) 7, 100
RSP_3341 RSP_3341 Protein of unknown function UPF0074 (NCBI) 85, 172
RSP_3595 metK S-adenosylmethionine synthetase (NCBI) 43, 85
RSP_3754 RSP_3754 hypothetical protein (NCBI) 21, 100
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_2835
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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