Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2825

pyruvate formate-lyase 1 activating enzyme

CircVis
Functional Annotations (9)
Function System
Pyruvate-formate lyase-activating enzyme cog/ cog
cytoplasm go/ cellular_component
glucose metabolic process go/ biological_process
electron transport go/ biological_process
oxygen and reactive oxygen species metabolic process go/ biological_process
electron carrier activity go/ molecular_function
[formate-C-acetyltransferase]-activating enzyme activity go/ molecular_function
4 iron, 4 sulfur cluster binding go/ molecular_function
PFLE_PFLC tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2825
(Mouseover regulator name to see its description)

DVU2825 is regulated by 15 influences and regulates 0 modules.
Regulators for DVU2825 (15)
Regulator Module Operator
DVU0606
DVU0269
222 combiner
DVU1584 222 tf
DVU1584
DVU0269
222 combiner
DVU2086
DVU0744
222 combiner
DVU2086
DVU3229
222 combiner
DVU2423
DVU0744
222 combiner
DVU2532 222 tf
DVU1063 214 tf
DVU1744 214 tf
DVU2785
DVU1517
214 combiner
DVU2785
DVU2195
214 combiner
DVU2953
DVU2960
214 combiner
DVU3023 214 tf
DVUA0024 214 tf
DVUA0057 214 tf

Warning: DVU2825 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
407 1.80e+02 Aac.caC.ACa.gAtAgGaA
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RegPredict
408 1.80e+01 CGCA.gAGGCATGAC
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RegPredict
423 4.80e-02 AataGACaTATaTGaAcTaaTGaA
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RegPredict
424 3.70e-03 actCctCcGtaaatcTgCacG
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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 DVU2825

DVU2825 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Pyruvate-formate lyase-activating enzyme cog/ cog
cytoplasm go/ cellular_component
glucose metabolic process go/ biological_process
electron transport go/ biological_process
oxygen and reactive oxygen species metabolic process go/ biological_process
electron carrier activity go/ molecular_function
[formate-C-acetyltransferase]-activating enzyme activity go/ molecular_function
4 iron, 4 sulfur cluster binding go/ molecular_function
PFLE_PFLC tigr/ tigrfam
Module neighborhood information for DVU2825

DVU2825 has total of 48 gene neighbors in modules 214, 222
Gene neighbors (48)
Gene Common Name Description Module membership
DVU0049 OmpA family protein 222, 247
DVU0131 hypothetical protein DVU0131 167, 222
DVU0132 hypothetical protein DVU0132 167, 222
DVU0133 hypothetical protein DVU0133 167, 222
DVU0195 hypothetical protein DVU0195 222, 314
DVU0229 hypothetical protein DVU0229 214, 296
DVU0288 None 107, 222
DVU0297 hypothetical protein DVU0297 214, 334
DVU0355 sensory box protein 222, 320
DVU0372 hypothetical protein DVU0372 53, 214
DVU0405 cobB-1 cobyrinic acid a,c-diamide synthase 126, 214
DVU0452 hypothetical protein DVU0452 106, 222
DVU0546 hypothetical protein DVU0546 126, 214
DVU0620 L-PSP family endoribonuclease 63, 214
DVU0623 hypothetical protein DVU0623 134, 222
DVU0644 hypothetical protein DVU0644 99, 222
DVU0652 cheV-2 chemotaxis protein CheV 83, 214
DVU0666 HD domain-containing protein 214, 309
DVU0940 GGDEF domain-containing protein 214, 303
DVU1739 hypothetical protein DVU1739 121, 214
DVU1825 amidohydrolase family protein 27, 214
DVU1838 trxB-2 thioredoxin-disulfide reductase 167, 222
DVU1860 lnt apolipoprotein N-acyltransferase 9, 214
DVU1989 hypothetical protein DVU1989 214, 309
DVU2257 hypothetical protein DVU2257 9, 214
DVU2391 hypothetical protein DVU2391 198, 214
DVU2478 pstC phosphate ABC transporter permease PstC 126, 214
DVU2584 CorA family protein 126, 214
DVU2666 phosphate ABC transporter permease 99, 214
DVU2761 hypothetical protein DVU2761 181, 214
DVU2825 pyruvate formate-lyase 1 activating enzyme 214, 222
DVU2843 DNA mismatch endonuclease Vsr 214, 334
DVU2844 hypothetical protein DVU2844 214, 334
DVU2884 aminopeptidase 1 62, 222
DVU2992 glycosyl transferase group 2 family protein 222, 341
DVU3023 sigma-54 dependent DNA-binding response regulator 23, 214
DVU3064 sensory box protein 176, 222
DVU3106 GGDEF domain-containing protein 36, 222
DVU3145 hydrogenase, b-type cytochrome subunit 214, 309
DVU3147 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 192, 214
DVU3195 lipoprotein 161, 214
DVU3196 twin-arginine translocation pathway signal sequence domain-containing protein 87, 214
DVU3321 hypothetical protein DVU3321 185, 222
DVU3322 hypothetical protein DVU3322 144, 222
DVU3323 ABC transporter permease 144, 222
DVU3324 ABC transporter ATP-binding protein 144, 222
DVU3386 permease 69, 222
DVUA0029 hypothetical protein DVUA0029 167, 222
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 DVU2825
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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