Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2328

hydrogenase nickel insertion protein HypA

CircVis
Functional Annotations (3)
Function System
Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) cog/ cog
protein modification process go/ biological_process
nickel ion binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2328
(Mouseover regulator name to see its description)

DVU2328 is regulated by 17 influences and regulates 0 modules.
Regulators for DVU2328 (17)
Regulator Module Operator
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
DVU0118
DVU2251
249 combiner
DVU0230 249 tf
DVU0230
DVU2989
249 combiner
DVU0653
DVU2251
249 combiner
DVU0854
DVU2251
249 combiner
DVU2686
DVU0118
249 combiner
DVU2989 249 tf
DVU3220
DVU2251
249 combiner

Warning: DVU2328 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
475 3.20e+01 cttcgc..t.tgtctTG.Cgc
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RegPredict
476 1.00e+04 TtgtTaTttTc.AgAaGTtT
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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 DVU2328

DVU2328 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) cog/ cog
protein modification process go/ biological_process
nickel ion binding go/ molecular_function
Module neighborhood information for DVU2328

DVU2328 has total of 54 gene neighbors in modules 145, 249
Gene neighbors (54)
Gene Common Name Description Module membership
DVU0041 Slt family transglycosylase 145, 146
DVU0092 sensory box histidine kinase 145, 348
DVU0121 hypothetical protein DVU0121 206, 249
DVU0521 csrA carbon storage regulator 184, 249
DVU0876 metallo-beta-lactamase family protein 145, 172
DVU0952 hypothetical protein DVU0952 52, 145
DVU1051 ccmE cytochrome c-type biogenesis protein CcmE 14, 249
DVU1057 cobalt ABC transporter permease 145, 309
DVU1058 cbiM cobalt transport protein CbiM 6, 145
DVU1283 galU UTP-glucose-1-phosphate uridylyltransferase 60, 249
DVU1372 hypothetical protein DVU1372 232, 249
DVU1373 divIVA cell-division initiation protein DivIVA 232, 249
DVU1374 hypothetical protein DVU1374 232, 249
DVU1375 hypothetical protein DVU1375 232, 249
DVU1377 ilvH acetolactate synthase 3 regulatory subunit 232, 249
DVU1378 ilvC ketol-acid reductoisomerase 232, 249
DVU1460 hypothetical protein DVU1460 145, 334
DVU1881 phoH family protein 12, 249
DVU1882 HDIG domain-containing protein 95, 249
DVU1883 hypothetical protein DVU1883 117, 249
DVU1887 hypothetical protein DVU1887 128, 249
DVU1910 YjeF-like protein 146, 249
DVU1937 phosphonate ABC transporter periplasmic phosphonate-binding protein 145, 262
DVU2083 relA GTP pyrophosphokinase 145, 318
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
DVU2430 RNA-binding protein 249, 296
DVU2508 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase 249, 301
DVU2509 murE UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase 249, 301
DVU2514 pyk pyruvate kinase 249, 348
DVU2580 response regulator 145, 251
DVU2612 hypothetical protein DVU2612 63, 249
DVU2619 hypothetical protein DVU2619 145, 162
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
DVU3045 sensory box histidine kinase/response regulator 11, 249
DVU3097 outer membrane efflux protein 141, 249
DVU3112 hypothetical protein 249, 315
DVU3113 carA carbamoyl phosphate synthase small subunit 14, 249
DVU3157 hypothetical protein DVU3157 145, 250
DVU3158 vacJ lipoprotein 26, 145
DVU3177 hypothetical protein DVU3177 145, 169
DVU3190 hypothetical protein DVU3190 145, 176
DVU3197 ilvE branched-chain amino acid aminotransferase 220, 249
DVU3221 sensor histidine kinase 115, 145
DVU3273 hypothetical protein DVU3273 145, 186
DVU3335 sensory box histidine kinase 162, 249
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 DVU2328
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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