Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0041

Slt family transglycosylase

CircVis
Functional Annotations (2)
Function System
FOG: LysM repeat cog/ cog
cell wall macromolecule catabolic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0041
(Mouseover regulator name to see its description)

DVU0041 is regulated by 20 influences and regulates 0 modules.
Regulators for DVU0041 (20)
Regulator Module Operator
DVU0057 146 tf
DVU0230 146 tf
DVU0525 146 tf
DVU0606
DVU1690
146 combiner
DVU1730 146 tf
DVU1745 146 tf
DVU2423
DVU0619
146 combiner
DVU2423
DVU1402
146 combiner
DVU2557
DVU1690
146 combiner
DVU2686 146 tf
DVU3193
DVU1690
146 combiner
DVU0110 145 tf
DVU0230 145 tf
DVU0653
DVU1063
145 combiner
DVU0653
DVU1690
145 combiner
DVU1517 145 tf
DVU1518
DVU2086
145 combiner
DVU1628 145 tf
DVU1754
DVU3381
145 combiner
DVU2532
DVU0653
145 combiner

Warning: DVU0041 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
277 3.80e-01 atttctTgaTTgatcAaACagttt
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RegPredict
278 1.90e+02 cCcTgAccAcGcAac
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RegPredict
279 5.10e-02 GcCaGcttcTACcGGa
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RegPredict
280 8.10e+04 C.ataCgc.T.tacTc.GtgAcgg
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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 DVU0041

DVU0041 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
FOG: LysM repeat cog/ cog
cell wall macromolecule catabolic process go/ biological_process
Module neighborhood information for DVU0041

DVU0041 has total of 57 gene neighbors in modules 145, 146
Gene neighbors (57)
Gene Common Name Description Module membership
DVU0041 Slt family transglycosylase 145, 146
DVU0092 sensory box histidine kinase 145, 348
DVU0841 aspartate aminotransferase 146, 344
DVU0876 metallo-beta-lactamase family protein 145, 172
DVU0896 NLP/P60 family lipoprotein 78, 146
DVU0899 hypothetical protein DVU0899 146, 172
DVU0936 hypothetical protein DVU0936 146, 232
DVU0952 hypothetical protein DVU0952 52, 145
DVU0965 hypothetical protein DVU0965 146, 215
DVU0966 amino acid ABC transporter periplasmic amino acid-binding protein 146, 306
DVU1038 hisA 1-(5-phosphoribosyl)-5- 146, 288
DVU1057 cobalt ABC transporter permease 145, 309
DVU1058 cbiM cobalt transport protein CbiM 6, 145
DVU1064 aconitate hydratase 14, 146
DVU1067 Bmp family membrane protein 146, 221
DVU1238 amino acid ABC transporter periplasmic amino acid-binding protein 146, 255
DVU1392 NLP/P60 family protein 146, 232
DVU1406 purM phosphoribosylaminoimidazole synthetase 88, 146
DVU1423 lpdA 2-oxoglutarate dehydrogenase, E3 component, lipoamide dehydrogenase 14, 146
DVU1460 hypothetical protein DVU1460 145, 334
DVU1615 paaK-2 phenylacetate-coenzyme A ligase 146, 323
DVU1910 YjeF-like protein 146, 249
DVU1937 phosphonate ABC transporter periplasmic phosphonate-binding protein 145, 262
DVU1954 nadD nicotinate (nicotinamide) nucleotide adenylyltransferase 56, 146
DVU1990 hypothetical protein DVU1990 146, 196
DVU2056 hypothetical protein DVU2056 54, 146
DVU2083 relA GTP pyrophosphokinase 145, 318
DVU2150 dnaK suppressor protein 146, 297
DVU2251 DNA-binding protein 135, 146
DVU2285 L-lactate permease family protein 145, 306
DVU2286 hydrogenase subunit CooM 145, 207
DVU2287 hydrogenase subunit CooK 145, 346
DVU2289 hydrogenase subunit CooX 145, 207
DVU2291 carbon monoxide-induced hydrogenase CooH 145, 207
DVU2328 hydrogenase nickel insertion protein HypA 145, 249
DVU2364 class I/II aminotransferase 146, 262
DVU2580 response regulator 145, 251
DVU2619 hypothetical protein DVU2619 145, 162
DVU2782 hypothetical protein DVU2782 26, 146
DVU2783 hypothetical protein DVU2783 146, 195
DVU2791 cytochrome c family protein 139, 146
DVU2940 hypothetical protein DVU2940 146, 215
DVU2944 ErfK/YbiS/YcfS/YnhG family protein 55, 145
DVU2945 hypothetical protein DVU2945 145, 278
DVU2980 pssA CDP-diacylglycerol--serine O-phosphatidyltransferase 145, 308
DVU3005 aminotransferase 22, 145
DVU3157 hypothetical protein DVU3157 145, 250
DVU3158 vacJ lipoprotein 26, 145
DVU3171 cytochrome c3 146, 262
DVU3177 hypothetical protein DVU3177 145, 169
DVU3187 hup-4 DNA-binding protein HU 146, 232
DVU3190 hypothetical protein DVU3190 145, 176
DVU3221 sensor histidine kinase 115, 145
DVU3238 response regulator 146, 157
DVU3273 hypothetical protein DVU3273 145, 186
DVU3277 hypothetical protein DVU3277 146, 337
DVUA0138 sensor histidine kinase 145, 185
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 DVU0041
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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