Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0444

CBS domain-containing protein

CircVis
Functional Annotations (2)
Function System
catalytic activity go/ molecular_function
metabolic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0444
(Mouseover regulator name to see its description)

DVU0444 is regulated by 25 influences and regulates 0 modules.
Regulators for DVU0444 (25)
Regulator Module Operator
DVU0230 264 tf
DVU0525 264 tf
DVU0653 264 tf
DVU0653
DVU2633
264 combiner
DVU1517 264 tf
DVU1561
DVUA0143
264 combiner
DVU1754 264 tf
DVU2423
DVU2832
264 combiner
DVU2532
DVU0653
264 combiner
DVU2588 264 tf
DVU3142 264 tf
DVU3142
DVU0529
264 combiner
DVUA0024 264 tf
DVUA0143 264 tf
DVU0030
DVU2567
19 combiner
DVU0230 19 tf
DVU0230
DVU0621
19 combiner
DVU0653
DVU2114
19 combiner
DVU1063 19 tf
DVU1561
DVUA0143
19 combiner
DVU1754 19 tf
DVU2423
DVU2832
19 combiner
DVU2423
DVU3142
19 combiner
DVU2832 19 tf
DVU2836
DVU0653
19 combiner

Warning: DVU0444 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.
Click on the RegPredict links to explore the motif in RegPredict.

Motif Table (4)
Motif Id e-value Consensus Motif Logo RegPredict
37 1.40e+03 atgCCtcAtcggCAaGacgC
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RegPredict
38 1.70e+04 AAAaTACACAT
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RegPredict
503 5.00e+02 cgCTaCaGgct
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RegPredict
504 1.30e+03 tgcttcCTgtCa.g
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RegPredict
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 DVU0444

DVU0444 is enriched for 2 functions in 2 categories.
Enrichment Table (2)
Function System
catalytic activity go/ molecular_function
metabolic process go/ biological_process
Module neighborhood information for DVU0444

DVU0444 has total of 25 gene neighbors in modules 19, 264
Gene neighbors (25)
Gene Common Name Description Module membership
DVU0016 hypothetical protein DVU0016 47, 264
DVU0367 Ser/Thr protein phosphatase family protein 19, 68
DVU0444 CBS domain-containing protein 19, 264
DVU0447 hypothetical protein DVU0447 13, 19
DVU0486 hypothetical protein DVU0486 19, 36
DVU0609 lipoprotein 19, 118
DVU0892 aroL shikimate kinase II 19, 32
DVU0964 Glu/Leu/Phe/Val dehydrogenase family protein 1, 19
DVU1265 hypothetical protein DVU1265 264, 295
DVU1695 tail fiber assembly protein 168, 264
DVU1884 methyl-accepting chemotaxis protein 19, 149
DVU1962 methyl-accepting chemotaxis protein 1, 19
DVU1982 rhlE ATP-dependent RNA helicase RhlE 19, 85
DVU2192 hypothetical protein DVU2192 47, 264
DVU2218 GTP-binding protein 203, 264
DVU2595 hypothetical protein DVU2595 149, 264
DVU2631 hypothetical protein DVU2631 264, 295
DVU2740 livF high-affinity branched-chain amino acid ABC transporter ATP-binding protein 72, 264
DVU2754 qor quinone oxidoreductase 264, 295
DVU2828 phage integrase family site specific recombinase 19, 264
DVU3152 sensory box histidine kinase 19, 102
DVU3169 cbiG cobalamin biosynthesis protein CbiG 19, 124
DVU3251 HPP family membrane protein 3, 264
DVU3354 None 19, 217
DVU3370 hypothetical protein DVU3370 182, 264
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 DVU0444
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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