Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2985 leuB

3-isopropylmalate dehydrogenase

CircVis
Functional Annotations (8)
Function System
Isocitrate/isopropylmalate dehydrogenase cog/ cog
3-isopropylmalate dehydrogenase activity go/ molecular_function
cytoplasm go/ cellular_component
leucine biosynthetic process go/ biological_process
Valine leucine and isoleucine biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
leuB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2985
(Mouseover regulator name to see its description)

DVU2985 is regulated by 16 influences and regulates 0 modules.
Regulators for DVU2985 leuB (16)
Regulator Module Operator
DVU0309
DVU3229
46 combiner
DVU0744
DVU1730
46 combiner
DVU0936
DVU1759
46 combiner
DVU1759 46 tf
DVU2644
DVU0936
46 combiner
DVU2953 46 tf
DVU3229
DVU1730
46 combiner
DVU3381
DVU1730
46 combiner
DVU0269 103 tf
DVU1517 103 tf
DVU2567
DVU2675
103 combiner
DVU2802
DVU0110
103 combiner
DVU2802
DVU3229
103 combiner
DVU2909
DVU1628
103 combiner
DVU3111
DVU0309
103 combiner
DVUA0100 103 tf

Warning: DVU2985 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
91 6.40e-02 tGCGAcaT.ttTtTaCGAAaa
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RegPredict
92 2.20e+02 ccgACcacgCacCgc
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RegPredict
199 3.50e+02 gTGCc.CacCacgatacGAC
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RegPredict
200 9.70e+02 gcgCAgcCTcaCac.aca
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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 DVU2985

DVU2985 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Isocitrate/isopropylmalate dehydrogenase cog/ cog
3-isopropylmalate dehydrogenase activity go/ molecular_function
cytoplasm go/ cellular_component
leucine biosynthetic process go/ biological_process
Valine leucine and isoleucine biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
leuB tigr/ tigrfam
Module neighborhood information for DVU2985

DVU2985 has total of 38 gene neighbors in modules 46, 103
Gene neighbors (38)
Gene Common Name Description Module membership
DVU0036 hypothetical protein DVU0036 5, 103
DVU0051 hypothetical protein DVU0051 26, 46
DVU0245 protein phosphatase 46, 304
DVU0282 mutY A/G-specific adenine glycosylase 46, 228
DVU0344 methyl-accepting chemotaxis protein 81, 103
DVU0345 hypothetical protein DVU0345 46, 69
DVU0412 potassium uptake protein TrkA 46, 304
DVU0499 hypothetical protein DVU0499 46, 62
DVU0567 TerC family protein 103, 116
DVU0590 hypothetical protein DVU0590 46, 120
DVU0601 phenylacetic acid degradation protein PaaI 46, 281
DVU0616 hypothetical protein DVU0616 46, 309
DVU0637 hypothetical protein DVU0637 30, 103
DVU0645 methyl-accepting chemotaxis protein 103, 331
DVU1097 hypothetical protein DVU1097 46, 127
DVU1259 hypothetical protein DVU1259 46, 99
DVU1668 outer membrane lipoprotein carrier protein 46, 178
DVU1953 proA gamma-glutamyl phosphate reductase 46, 62
DVU2090 EF hand domain-containing protein 46, 247
DVU2093 thiH thiamine biosynthesis protein ThiH 46, 238
DVU2211 hypothetical protein DVU2211 103, 184
DVU2359 sigma-54 dependent transcriptional regulator 12, 46
DVU2437 ABC transporter permease 46, 267
DVU2473 hypothetical protein DVU2473 37, 46
DVU2474 hypothetical protein DVU2474 46, 123
DVU2475 ferredoxin-NADP(+) reductase subunit alpha 46, 62
DVU2971 glycosyl transferase family protein 103, 254
DVU2979 phosphatidylserine decarboxylase 103, 166
DVU2981 leuA 2-isopropylmalate synthase 46, 103
DVU2982 3-isopropylmalate dehydratase large subunit 46, 103
DVU2983 leuD 3-isopropylmalate dehydratase small subunit 46, 103
DVU2984 hypothetical protein DVU2984 46, 103
DVU2985 leuB 3-isopropylmalate dehydrogenase 46, 103
DVU3087 cobH precorrin-8X methylmutase 46, 141
DVU3287 glycosyl transferase group 2 family protein 46, 150
DVU3292 pyridine nucleotide-disulfide oxidoreductase 46, 280
DVU3383 hypothetical protein DVU3383 103, 127
DVU3385 hypothetical protein DVU3385 31, 103
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 DVU2985
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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