Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0938

isoamylase N-terminal domain-containing protein

CircVis
Functional Annotations (2)
Function System
hydrolase activity, hydrolyzing O-glycosyl compounds go/ molecular_function
carbohydrate metabolic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0938
(Mouseover regulator name to see its description)

DVU0938 is regulated by 24 influences and regulates 0 modules.
Regulators for DVU0938 (24)
Regulator Module Operator
DVU1144 132 tf
DVU1730 132 tf
DVU1788 132 tf
DVU2394 132 tf
DVU2557 132 tf
DVU2557
DVU1628
132 combiner
DVU2557
DVU2675
132 combiner
DVU2675
DVU2251
132 combiner
DVU2686 132 tf
DVU2788
DVU2114
132 combiner
DVU2989 132 tf
DVU0110 71 tf
DVU1331 71 tf
DVU1572
DVU0629
71 combiner
DVU1572
DVU2394
71 combiner
DVU1572
DVU2547
71 combiner
DVU1788 71 tf
DVU2557
DVU2675
71 combiner
DVU2567 71 tf
DVU2675 71 tf
DVU2675
DVU1144
71 combiner
DVU2788 71 tf
DVU2788
DVU2557
71 combiner
DVU3084 71 tf

Warning: DVU0938 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
139 6.00e+02 AgCatgaAtGGA..tGaag
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RegPredict
140 1.30e+04 TGacgcTcTcGAAaTaAC.cCTT
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RegPredict
255 3.90e+03 AAGGaGga
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RegPredict
256 5.80e+03 GcttctCcaCcgTaTCGaaGA
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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 DVU0938

DVU0938 is enriched for 2 functions in 2 categories.
Enrichment Table (2)
Function System
hydrolase activity, hydrolyzing O-glycosyl compounds go/ molecular_function
carbohydrate metabolic process go/ biological_process
Module neighborhood information for DVU0938

DVU0938 has total of 47 gene neighbors in modules 71, 132
Gene neighbors (47)
Gene Common Name Description Module membership
DVU0006 universal stress protein 132, 148
DVU0042 RNA methyltransferase 6, 132
DVU0138 response regulator 132, 148
DVU0238 hypothetical protein DVU0238 132, 148
DVU0275 polysaccharide deacetylase family protein 71, 308
DVU0276 hypothetical protein DVU0276 60, 71
DVU0305 ferredoxin II 132, 148
DVU0453 ATP-dependent DNA helicase UvrD 71, 274
DVU0565 gap-1 glyceraldehyde 3-phosphate dehydrogenase 60, 71
DVU0566 GAF domain-containing protein 60, 71
DVU0629 TetR family transcriptional regulator 132, 272
DVU0754 hypothetical protein DVU0754 71, 132
DVU0938 isoamylase N-terminal domain-containing protein 71, 132
DVU0974 hypothetical protein DVU0974 60, 132
DVU0986 hypothetical protein DVU0986 132, 232
DVU0987 heavy metal-binding domain-containing protein 132, 232
DVU1093 HAD family hydrolase 132, 232
DVU1180 hypothetical protein DVU1180 71, 132
DVU1244 hypothetical protein DVU1244 16, 71
DVU1449 anti-anti-sigma factor 71, 318
DVU1450 anti-sigma factor 71, 318
DVU1470 ppiC peptidyl-prolyl cis-trans isomerase C 132, 343
DVU1471 HSP20 family protein 71, 192
DVU1528 cytidine/deoxycytidylate deaminase family protein 60, 71
DVU1529 decarboxylase 60, 71
DVU1568 ferritin 132, 148
DVU1656 folK 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase 16, 71
DVU1817 cyf cytochrome c-553 132, 175
DVU1867 dapF diaminopimelate epimerase 16, 71
DVU1894 hypothetical protein DVU1894 132, 332
DVU1904 cheW-2 chemotaxis protein CheW 132, 148
DVU2059 glycosyl transferase group 2 family protein 71, 225
DVU2060 hypothetical protein DVU2060 33, 71
DVU2076 cheR-2 chemotaxis protein methyltransferase 132, 148
DVU2202 transglycosylase 132, 148
DVU2212 hypothetical protein DVU2212 60, 132
DVU2351 hypothetical protein DVU2351 132, 272
DVU2427 hypothetical protein DVU2427 60, 71
DVU2625 hypothetical protein DVU2625 132, 225
DVU2684 hypothetical protein DVU2684 71, 148
DVU2770 response regulator 71, 229
DVU2840 hypothetical protein DVU2840 71, 111
DVU2935 gpmA phosphoglyceromutase 71, 148
DVU2937 TPR domain/response regulator receiver domain-containing protein 71, 229
DVU2973 integration host factor subunit beta 132, 175
DVU3226 hypothetical protein DVU3226 71, 332
DVU3227 flagellar basal body-associated protein 71, 148
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 DVU0938
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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