Organism : Geobacter sulfurreducens | Module List :
GSU3021

DegT/DnrJ/EryC1/StrS family protein (VIMSS)

CircVis
Functional Annotations (3)
Function System
Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis cog/ cog
catalytic activity go/ molecular_function
pyridoxal phosphate binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3021
(Mouseover regulator name to see its description)

GSU3021 is regulated by 19 influences and regulates 0 modules.
Regulators for GSU3021 (19)
Regulator Module Operator
GSU0187 138 tf
GSU0581 138 tf
GSU0732 138 tf
GSU0896 138 tf
GSU1013 138 tf
GSU2506 138 tf
GSU2520 138 tf
GSU2753 138 tf
GSU2787 138 tf
GSU3053 138 tf
GSU3109 138 tf
GSU0359 27 tf
GSU1201 27 tf
GSU1218 27 tf
GSU1410 27 tf
GSU1626 27 tf
GSU1687 27 tf
GSU1992 27 tf
GSU2581 27 tf

Warning: GSU3021 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
2214 5.20e+01 Cc.ctCAtCaCCcTcAAgGagG
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2215 3.50e+02 tttGAtttTcCTGAT
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2436 1.90e+01 gCcaTTtgCAt.aaa.a.gAt
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2437 4.70e+03 AAaaCACTGcA.AC
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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 GSU3021

GSU3021 is enriched for 3 functions in 3 categories.
Module neighborhood information for GSU3021

GSU3021 has total of 40 gene neighbors in modules 27, 138
Gene neighbors (40)
Gene Common Name Description Module membership
GSU0293 cheB-1 protein-glutamate methylesterase (NCBI) 127, 138
GSU0297 cheW-1 purine-binding chemotaxis protein CheW (NCBI) 49, 138
GSU0719 GSU0719 hypothetical protein (VIMSS) 27, 311
GSU0827 GSU0827 hypothetical protein (VIMSS) 27, 53
GSU0828 GSU0828 metal ion efflux outer membrane protein family protein, putative (VIMSS) 27, 92
GSU0829 GSU0829 heavy metal efflux pump, CzcB family (VIMSS) 27, 53
GSU0830 GSU0830 heavy metal efflux pump, CzcA family (VIMSS) 27, 155
GSU0831 GSU0831 nitrogen regulatory protein P-II, putative (VIMSS) 27, 180
GSU0909 GSU0909 pyridine nucleotide-disulphide oxidoreductase family protein (NCBI) 138, 237
GSU0912 GSU0912 hypothetical protein (VIMSS) 127, 138
GSU1307 ftn ferritin (NCBI) 27, 85
GSU1560 GSU1560 radical SAM domain protein (NCBI) 138, 240
GSU1642 GSU1642 conserved hypothetical protein (VIMSS) 27, 53
GSU1646 GSU1646 lipoprotein, putative (VIMSS) 27, 172
GSU1661 GSU1661 hypothetical protein (VIMSS) 27, 118
GSU2034 GSU2034 hypothetical protein (VIMSS) 23, 138
GSU2035 GSU2035 hypothetical protein (NCBI) 20, 138
GSU2036 GSU2036 hypothetical protein (VIMSS) 23, 138
GSU2037 GSU2037 hypothetical protein (VIMSS) 23, 138
GSU2038 GSU2038 hypothetical protein (NCBI) 23, 138
GSU2039 GSU2039 hypothetical protein (VIMSS) 23, 138
GSU2322 GSU2322 hypothetical protein (VIMSS) 13, 27
GSU2324 GSU2324 hypothetical protein (VIMSS) 27, 175
GSU2325 GSU2325 cation-transport ATPase, E1-E2 family (VIMSS) 27, 261
GSU2584 GSU2584 lipoprotein, putative (VIMSS) 138, 237
GSU2595 GSU2595 hypothetical protein (VIMSS) 27, 295
GSU2653 GSU2653 MATE efflux family protein (VIMSS) 27, 34
GSU2654 pdhA pyruvate dehydrogenase complex E1 component, alpha subunit (NCBI) 27, 109
GSU2691 GSU2691 conserved hypothetical protein (VIMSS) 27, 85
GSU3018 GSU3018 conserved hypothetical protein (VIMSS) 27, 257
GSU3019 GSU3019 dehydrogenase, E1 component, alpha and beta subunits (NCBI) 27, 96
GSU3021 GSU3021 DegT/DnrJ/EryC1/StrS family protein (VIMSS) 27, 138
GSU3022 GSU3022 hypothetical protein (NCBI) 27, 138
GSU3024 GSU3024 hypothetical protein (VIMSS) 27, 138
GSU3025 GSU3025 heptosyltransferase family protein (VIMSS) 27, 272
GSU3051 flgG-1 flagellar basal-body rod protein FlgG (NCBI) 23, 138
GSU3279 uvrC excinuclease ABC, C subunit (NCBI) 137, 138
GSU3326 GSU3326 conserved hypothetical protein (VIMSS) 27, 311
GSU3327 GSU3327 conserved hypothetical protein (VIMSS) 27, 85
GSU3344 GSU3344 hypothetical protein (VIMSS) 27, 279
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 GSU3021
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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