Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0055 ispH

hydroxymethylbutenyl pyrophosphate reductase

CircVis
Functional Annotations (7)
Function System
Penicillin tolerance protein cog/ cog
isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway go/ biological_process
4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase activity go/ molecular_function
Terpenoid backbone biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
ispH_lytB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0055
(Mouseover regulator name to see its description)

DVU0055 is regulated by 22 influences and regulates 0 modules.
Regulators for DVU0055 ispH (22)
Regulator Module Operator
DVU0110 185 tf
DVU0309 185 tf
DVU0309
DVU0946
185 combiner
DVU1144 185 tf
DVU1419 185 tf
DVU1517 185 tf
DVU1518 185 tf
DVU1518
DVU3080
185 combiner
DVU2114
DVU1063
185 combiner
DVU2319 185 tf
DVU2675
DVU1745
185 combiner
DVU2953
DVU1402
185 combiner
DVU1645
DVU3193
304 combiner
DVU1674
DVU3095
304 combiner
DVU1674
DVU3186
304 combiner
DVU2319 304 tf
DVU2547
DVU2934
304 combiner
DVU2644 304 tf
DVU2644
DVU2799
304 combiner
DVU2934
DVU0621
304 combiner
DVU3084 304 tf
DVU3193
DVU2114
304 combiner

Warning: DVU0055 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
353 6.90e-01 GC.TCGcAACG
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RegPredict
354 7.30e+03 CctTCCgGcAG
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RegPredict
581 5.20e+04 TcCATGTCacA
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RegPredict
582 2.00e+04 CggaTGCCCTG
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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 DVU0055

DVU0055 is enriched for 7 functions in 3 categories.
Module neighborhood information for DVU0055

DVU0055 has total of 58 gene neighbors in modules 185, 304
Gene neighbors (58)
Gene Common Name Description Module membership
DVU0029 hydantoinase/oxoprolinase family protein 162, 185
DVU0045 flagellar biosynthesis protein, FliO 185, 286
DVU0048 chemotaxis protein MotB 185, 267
DVU0055 ispH hydroxymethylbutenyl pyrophosphate reductase 185, 304
DVU0059 AcrB/AcrD/AcrF family protein 185, 316
DVU0130 phosphoglycolate phosphatase 185, 247
DVU0134 glycosyl transferase group 2 family protein 144, 185
DVU0187 GGDEF domain-containing protein 258, 304
DVU0245 protein phosphatase 46, 304
DVU0292 hypothetical protein DVU0292 162, 185
DVU0392 aromatic aminotransferase 37, 185
DVU0400 hypothetical protein DVU0400 185, 292
DVU0412 potassium uptake protein TrkA 46, 304
DVU0584 transposase 105, 304
DVU0661 dihydrouridine synthase family protein 87, 185
DVU0687 tungsten-containing aldehyde:ferredoxin oxidoreductase 82, 304
DVU0688 hypothetical protein DVU0688 185, 277
DVU0689 rnhA ribonuclease H 82, 304
DVU0723 purT phosphoribosylglycinamide formyltransferase 2 185, 278
DVU0749 DNA-binding response regulator 26, 304
DVU0818 hypothetical protein DVU0818 185, 267
DVU0897 RNA modification protein 172, 304
DVU0898 hypothetical protein DVU0898 172, 304
DVU0900 gmk guanylate kinase 172, 304
DVU0901 pyrF orotidine 5`-phosphate decarboxylase 32, 304
DVU0922 cytochrome c family protein 304, 307
DVU0996 hypothetical protein DVU0996 304, 307
DVU1113 hypothetical protein DVU1113 69, 185
DVU1160 urea transporter 161, 185
DVU1188 hypothetical protein DVU1188 211, 304
DVU1507 hypothetical protein DVU1507 185, 225
DVU1536 Slt family transglycosylase 12, 304
DVU2080 None 185, 316
DVU2092 thiamine biosynthesis protein ThiF 161, 304
DVU2233 hypothetical protein DVU2233 35, 185
DVU2234 hypothetical protein DVU2234 69, 185
DVU2365 hypothetical protein DVU2365 304, 315
DVU2413 radical SAM domain-containing protein 141, 185
DVU2477 pstS phosphate ABC transporter periplasmic phosphate-binding protein PstS 211, 304
DVU2479 phosphate ABC transporter permease 211, 304
DVU2493 iron-sulfur cluster-binding protein 185, 223
DVU2520 hypothetical protein DVU2520 69, 185
DVU2543 hydroxylamine reductase 153, 304
DVU2739 pyruvate phosphate dikinase PEP/pyruvate binding subunit 112, 304
DVU2749 cobL precorrin-6Y C5,15-methyltransferase (decarboxylating) 166, 304
DVU2759 hypothetical protein DVU2759 83, 185
DVU2821 hypothetical protein DVU2821 185, 316
DVU2886 AraC family transcriptional regulator 251, 304
DVU2947 anaerobic ribonucleoside triphosphate reductase 81, 304
DVU2961 hypothetical protein DVU2961 285, 304
DVU3010 aminotransferase 112, 304
DVU3074 hypothetical protein DVU3074 185, 316
DVU3091 hypothetical protein DVU3091 185, 316
DVU3229 fliA RNA polymerase sigma factor for flagellar operon FliA 251, 304
DVU3321 hypothetical protein DVU3321 185, 222
DVU3369 hypothetical protein DVU3369 185, 315
DVUA0072 glycosyl transferase, group 1 family protein 255, 304
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 DVU0055
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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