Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1958

sensory box histidine kinase

CircVis
Functional Annotations (7)
Function System
Signal transduction histidine kinase, nitrogen specific cog/ cog
two-component sensor activity go/ molecular_function
ATP binding go/ molecular_function
signal transduction go/ biological_process
membrane go/ cellular_component
peptidyl-histidine phosphorylation go/ biological_process
sensory_box tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1958
(Mouseover regulator name to see its description)

DVU1958 is regulated by 22 influences and regulates 0 modules.
Regulators for DVU1958 (22)
Regulator Module Operator
DVU1063 69 tf
DVU1063
DVU2934
69 combiner
DVU1744 69 tf
DVU2633
DVU1730
69 combiner
DVU2788
DVU1744
69 combiner
DVU3066
DVU2690
69 combiner
DVU3111
DVU1402
69 combiner
DVU3142
DVU0529
69 combiner
DVUA0100
DVU1063
69 combiner
DVU0110
DVU1419
192 combiner
DVU1572
DVU2547
192 combiner
DVU2275 192 tf
DVU2527
DVU1949
192 combiner
DVU2547 192 tf
DVU2547
DVU0110
192 combiner
DVU2547
DVU2675
192 combiner
DVU2547
DVU2799
192 combiner
DVU2557 192 tf
DVU2557
DVU2675
192 combiner
DVU2675 192 tf
DVU2909 192 tf
DVU3066 192 tf

Warning: DVU1958 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
135 1.60e+02 ttCattcTcttttccgGtcgCgca
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RegPredict
136 4.40e+03 ATGACa
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RegPredict
367 1.00e-02 gGcttTGGCGT
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RegPredict
368 4.20e+02 GCAtCGcAtgt
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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 DVU1958

DVU1958 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Signal transduction histidine kinase, nitrogen specific cog/ cog
two-component sensor activity go/ molecular_function
ATP binding go/ molecular_function
signal transduction go/ biological_process
membrane go/ cellular_component
peptidyl-histidine phosphorylation go/ biological_process
sensory_box tigr/ tigrfam
Module neighborhood information for DVU1958

DVU1958 has total of 75 gene neighbors in modules 69, 192
Gene neighbors (75)
Gene Common Name Description Module membership
DVU0038 acyltransferase domain-containing protein 69, 161
DVU0088 panF sodium/panthothenate symporter 9, 69
DVU0101 UbiE/COQ5 family methlytransferase 69, 247
DVU0104 cation ABC transporter permease 69, 162
DVU0175 tungsten formylmethanofuran dehydrogenase family protein/molybdopterin binding protein 192, 348
DVU0236 phage integrase family site specific recombinase 54, 69
DVU0249 hypothetical protein DVU0249 69, 181
DVU0257 acetyltransferase 37, 69
DVU0345 hypothetical protein DVU0345 46, 69
DVU0456 DHH family protein 153, 192
DVU0580 moaA molybdenum cofactor biosynthesis protein A 192, 281
DVU0600 ldh L-lactate dehydrogenase 192, 281
DVU0626 ilvN-1 acetolactate synthase small subunit 192, 298
DVU0627 ptB phosphotransbutyrylase 192, 229
DVU0701 glcB malate synthase G 192, 348
DVU0859 hypothetical protein DVU0859 69, 162
DVU1036 hypothetical protein DVU1036 69, 334
DVU1037 mercuric reductase 181, 192
DVU1113 hypothetical protein DVU1113 69, 185
DVU1165 pyridine nucleotide-disulfide oxidoreductase 69, 330
DVU1213 rhomboid family protein 69, 120
DVU1269 hypothetical protein DVU1269 69, 172
DVU1389 hypothetical protein DVU1389 69, 162
DVU1391 hypothetical protein DVU1391 69, 87
DVU1396 hypothetical protein DVU1396 192, 274
DVU1413 hypothetical protein DVU1413 192, 296
DVU1420 Hpt domain-containing protein 109, 192
DVU1435 hypothetical protein DVU1435 69, 87
DVU1471 HSP20 family protein 71, 192
DVU1472 ATP-dependent protease 115, 192
DVU1592 arginine N-succinyltransferase subunit beta 192, 274
DVU1594 cheA-1 chemotaxis protein CheA 192, 274
DVU1596 cheB-1 protein-glutamate methylesterase CheB 192, 274
DVU1613 glutamate synthase subunit beta 192, 236
DVU1614 iron-sulfur cluster-binding protein 6, 192
DVU1958 sensory box histidine kinase 69, 192
DVU1986 hypothetical protein DVU1986 192, 198
DVU2234 hypothetical protein DVU2234 69, 185
DVU2276 hypothetical protein DVU2276 69, 334
DVU2349 carbohydrate phosphorylase family protein 60, 192
DVU2360 FAD/NAD-binding family oxidoreductase 115, 192
DVU2366 hypothetical protein DVU2366 69, 155
DVU2408 hypothetical protein DVU2408 69, 269
DVU2421 4-oxalocrotonate tautomerase family protein 192, 274
DVU2422 nitroreductase family protein 192, 274
DVU2461 oligopeptide ABC transporter permease 9, 69
DVU2465 hypothetical protein DVU2465 69, 245
DVU2482 fdnG-2 formate dehydrogenase subunit alpha, selenocysteine-containing 192, 348
DVU2520 hypothetical protein DVU2520 69, 185
DVU2570 GGDEF domain/HAMP domain-containing protein 69, 247
DVU2594 hypothetical protein DVU2594 69, 275
DVU2660 hypothetical protein DVU2660 69, 275
DVU2700 hypothetical protein DVU2700 33, 69
DVU2780 hypothetical protein DVU2780 69, 141
DVU2823 TRAP transporter subunit DctMQ 69, 181
DVU2895 hypothetical protein DVU2895 115, 192
DVU2908 hypothetical protein DVU2908 69, 334
DVU2910 hypothetical protein DVU2910 69, 113
DVU2953 GntR family transcriptional regulator 35, 69
DVU2954 GGDEF domain-containing protein 69, 334
DVU2955 hypothetical protein DVU2955 69, 334
DVU2968 sensor histidine kinase/response regulator 148, 192
DVU2976 hypothetical protein DVU2976 83, 192
DVU3017 hypothetical protein DVU3017 69, 87
DVU3037 rhodanese-like domain-containing protein 192, 348
DVU3040 hypothetical protein DVU3040 69, 181
DVU3077 AhpC/TSA family protein 192, 269
DVU3147 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 192, 214
DVU3148 malQ 4-alpha-glucanotransferase 27, 192
DVU3217 hypothetical protein DVU3217 109, 192
DVU3282 ADP-ribosylglycohydrolase family protein 109, 192
DVU3386 permease 69, 222
DVUA0021 hypothetical protein DVUA0021 61, 192
DVUA0023 ABC transporter permease 192, 274
DVUA0091 katA catalase 192, 274
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 DVU1958
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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