Organism : Geobacter sulfurreducens | Module List :
GSU2016

sensory box/GGDEF family protein (VIMSS)

CircVis
Functional Annotations (8)
Function System
Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain cog/ cog
two-component sensor activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
cyclic nucleotide biosynthetic process go/ biological_process
phosphorus-oxygen lyase activity go/ molecular_function
intracellular signal transduction go/ biological_process
sensory_box tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2016
(Mouseover regulator name to see its description)

GSU2016 is regulated by 19 influences and regulates 0 modules.
Regulators for GSU2016 (19)
Regulator Module Operator
GSU0178 221 tf
GSU0682 221 tf
GSU1320 221 tf
GSU1495 221 tf
GSU1569 221 tf
GSU1831 221 tf
GSU2041 221 tf
GSU2753 221 tf
GSU3324 221 tf
GSU0280 191 tf
GSU0366 191 tf
GSU0721 191 tf
GSU1268 191 tf
GSU1653 191 tf
GSU2113 191 tf
GSU2506 191 tf
GSU2670 191 tf
GSU2941 191 tf
GSU3457 191 tf

Warning: GSU2016 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
2542 1.50e+02 aGaacaAgaaA.aaA
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2543 1.00e+04 aaaTTgAgcAtATgA
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2602 2.00e+03 tTTttT.AAtTtttATttAa
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2603 2.50e+03 aa.ct.tttc.TaacGC.Aaaaa
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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 GSU2016

GSU2016 is enriched for 8 functions in 3 categories.
Module neighborhood information for GSU2016

GSU2016 has total of 42 gene neighbors in modules 191, 221
Gene neighbors (42)
Gene Common Name Description Module membership
GSU0232 GSU0232 hypothetical protein (VIMSS) 191, 254
GSU0316 GSU0316 hypothetical protein (VIMSS) 8, 191
GSU0456 GSU0456 membrane protein, putative (VIMSS) 174, 221
GSU0603 GSU0603 hypothetical protein (VIMSS) 191, 254
GSU1120 GSU1120 response regulator (VIMSS) 218, 221
GSU1123 GSU1123 metallo-beta-lactamase family protein (VIMSS) 218, 221
GSU1152 GSU1152 conserved hypothetical protein (VIMSS) 218, 221
GSU1286 cheY-2 chemotaxis protein CheY (NCBI) 198, 221
GSU1443 GSU1443 sensor histidine kinase/response regulator (VIMSS) 183, 191
GSU1453 GSU1453 hypothetical protein (VIMSS) 191, 330
GSU1454 GSU1454 glycosyl transferase, group 2 family protein (VIMSS) 191, 330
GSU1456 GSU1456 conserved hypothetical protein (NCBI) 191, 330
GSU1457 GSU1457 polysaccharide deacetylase domain protein (NCBI) 191, 330
GSU1529 GSU1529 sensory box histidine kinase/response regulator (VIMSS) 42, 191
GSU1686 GSU1686 cytidine/deoxycytidylate deaminase family protein (VIMSS) 198, 221
GSU1725 GSU1725 nuclease SbcCD, C subunit, putative (NCBI) 218, 221
GSU1779 GSU1779 hypothetical protein (VIMSS) 221, 268
GSU1845 GSU1845 hypothetical protein (VIMSS) 191, 319
GSU1873 pepF oligoendopeptidase F (NCBI) 103, 191
GSU1950 GSU1950 capK related-protein (NCBI) 221, 268
GSU1951 GSU1951 conserved domain protein (VIMSS) 33, 221
GSU1952 GSU1952 hypothetical protein (VIMSS) 33, 221
GSU1960 GSU1960 hexapeptide transferase family protein (VIMSS) 191, 327
GSU1961 GSU1961 glycosyl transferase, group 2 family protein (VIMSS) 191, 254
GSU1962 GSU1962 glycosyl transferase, group 2 family protein (VIMSS) 88, 191
GSU1963 GSU1963 polysaccharide biosynthesis domain protein (VIMSS) 191, 327
GSU2016 GSU2016 sensory box/GGDEF family protein (VIMSS) 191, 221
GSU2017 GSU2017 conserved hypothetical protein (NCBI) 30, 221
GSU2018 gcvH-2 glycine cleavage system H protein (NCBI) 221, 309
GSU2019 accC acetyl-CoA carboxylase, biotin carboxylase (NCBI) 221, 309
GSU2022 aroQ 3-dehydroquinate dehydratase, type II (NCBI) 218, 221
GSU2024 GSU2024 hypothetical protein (VIMSS) 201, 221
GSU2026 aroK shikimate kinase (NCBI) 219, 221
GSU2172 GSU2172 OmpA domain protein, putative (VIMSS) 105, 191
GSU2611 GSU2611 hypothetical protein (VIMSS) 158, 191
GSU2888 GSU2888 B12-binding domain protein/radical SAM domain protein (NCBI) 221, 318
GSU2891 GSU2891 hypothetical protein (VIMSS) 108, 191
GSU3182 GSU3182 conserved domain protein (VIMSS) 191, 330
GSU3183 GSU3183 hypothetical protein (VIMSS) 191, 260
GSU3231 GSU3231 hypothetical protein (VIMSS) 218, 221
GSU3376 pleD GGDEF/response regulator receiver domain protein (NCBI) 201, 221
GSU3389 GSU3389 hypothetical protein (NCBI) 221, 282
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 GSU2016
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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