Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2625

hypothetical protein DVU2625

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2625
(Mouseover regulator name to see its description)

DVU2625 is regulated by 20 influences and regulates 0 modules.
Regulators for DVU2625 (20)
Regulator Module Operator
DVU1144 132 tf
DVU1730 132 tf
DVU1788 132 tf
DVU2394 132 tf
DVU2557 132 tf
DVU2557
DVU1628
132 combiner
DVU2557
DVU2675
132 combiner
DVU2675
DVU2251
132 combiner
DVU2686 132 tf
DVU2788
DVU2114
132 combiner
DVU2989 132 tf
DVU1331 225 tf
DVU1402 225 tf
DVU1402
DVU3381
225 combiner
DVU1584
DVU0653
225 combiner
DVU1584
DVU3066
225 combiner
DVU1628
DVU1744
225 combiner
DVU2036
DVU1063
225 combiner
DVU3313 225 tf
DVUA0100
DVU1949
225 combiner

Warning: DVU2625 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
255 3.90e+03 AAGGaGga
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RegPredict
256 5.80e+03 GcttctCcaCcgTaTCGaaGA
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RegPredict
429 1.50e+03 AaccTaacG.AaAaAata
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RegPredict
430 2.60e+04 AgGcAGAg
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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 DVU2625

Warning: No Functional annotations were found!

Module neighborhood information for DVU2625

DVU2625 has total of 48 gene neighbors in modules 132, 225
Gene neighbors (48)
Gene Common Name Description Module membership
DVU0006 universal stress protein 132, 148
DVU0042 RNA methyltransferase 6, 132
DVU0138 response regulator 132, 148
DVU0178 None 160, 225
DVU0228 hypothetical protein DVU0228 225, 313
DVU0238 hypothetical protein DVU0238 132, 148
DVU0305 ferredoxin II 132, 148
DVU0537 hypothetical protein DVU0537 225, 309
DVU0629 TetR family transcriptional regulator 132, 272
DVU0641 hypothetical protein DVU0641 37, 225
DVU0754 hypothetical protein DVU0754 71, 132
DVU0798 hypothetical protein DVU0798 225, 320
DVU0800 hypothetical protein DVU0800 62, 225
DVU0938 isoamylase N-terminal domain-containing protein 71, 132
DVU0955 alr alanine racemase 110, 225
DVU0962 hypothetical protein DVU0962 144, 225
DVU0974 hypothetical protein DVU0974 60, 132
DVU0986 hypothetical protein DVU0986 132, 232
DVU0987 heavy metal-binding domain-containing protein 132, 232
DVU1016 hypothetical protein DVU1016 225, 279
DVU1093 HAD family hydrolase 132, 232
DVU1180 hypothetical protein DVU1180 71, 132
DVU1388 hypothetical protein DVU1388 92, 225
DVU1402 LysR family transcriptional regulator 27, 225
DVU1418 sensory box histidine kinase 225, 281
DVU1470 ppiC peptidyl-prolyl cis-trans isomerase C 132, 343
DVU1507 hypothetical protein DVU1507 185, 225
DVU1566 phosphoadenosine phosphosulfate reductase 161, 225
DVU1568 ferritin 132, 148
DVU1817 cyf cytochrome c-553 132, 175
DVU1894 hypothetical protein DVU1894 132, 332
DVU1904 cheW-2 chemotaxis protein CheW 132, 148
DVU2058 HDIG domain-containing protein 225, 330
DVU2059 glycosyl transferase group 2 family protein 71, 225
DVU2076 cheR-2 chemotaxis protein methyltransferase 132, 148
DVU2091 thiE-1 thiamine-phosphate pyrophosphorylase 198, 225
DVU2202 transglycosylase 132, 148
DVU2212 hypothetical protein DVU2212 60, 132
DVU2351 hypothetical protein DVU2351 132, 272
DVU2528 hypothetical protein DVU2528 225, 313
DVU2587 sensor histidine kinase 225, 260
DVU2625 hypothetical protein DVU2625 132, 225
DVU2746 hypothetical protein DVU2746 225, 309
DVU2810 formate dehydrogenase formation protein FdhE 225, 305
DVU2826 hypothetical protein DVU2826 225, 313
DVU2969 acetoacetyl-CoA synthase 225, 279
DVU2973 integration host factor subunit beta 132, 175
DVU3288 hypothetical protein DVU3288 225, 331
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 DVU2625
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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