Organism : Geobacter sulfurreducens | Module List :
GSU2354

transcriptional regulator, IclR family (VIMSS)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2354
(Mouseover regulator name to see its description)

GSU2354 is regulated by 16 influences and regulates 10 modules.
Regulators for GSU2354 (16)
Regulator Module Operator
GSU0359 49 tf
GSU0581 49 tf
GSU1003 49 tf
GSU1626 49 tf
GSU2354 49 tf
GSU2506 49 tf
GSU2670 49 tf
GSU2753 49 tf
GSU3053 49 tf
GSU3396 49 tf
GSU1201 236 tf
GSU1522 236 tf
GSU1626 236 tf
GSU1989 236 tf
GSU3217 236 tf
GSU3421 236 tf

Warning: GSU2354 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
2258 2.40e+00 aCcGC.CCcGc
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2259 2.80e+04 TTTGACACCTtTTTGT
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2632 6.20e+02 AttgAaAtTaAcGgatACTTAt
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2633 2.50e+04 aAtCTCcggAtatgacgAaaaaat
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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 GSU2354

GSU2354 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for GSU2354

GSU2354 has total of 48 gene neighbors in modules 49, 236
Gene neighbors (48)
Gene Common Name Description Module membership
GSU0219 GSU0219 cytochrome c oxidase, subunit I (VIMSS) 49, 237
GSU0220 GSU0220 cytochrome c oxidase, subunit III (VIMSS) 49, 310
GSU0221 GSU0221 cytochrome c oxidase, subunit IV (VIMSS) 49, 237
GSU0287 GSU0287 HD domain protein (VIMSS) 49, 133
GSU0288 GSU0288 PBS lyase HEAT-like repeat protein (NCBI) 210, 236
GSU0297 cheW-1 purine-binding chemotaxis protein CheW (NCBI) 49, 138
GSU0430 GSU0430 tail lysozyme, putative (NCBI) 86, 236
GSU0492 xerD site-specific recombinase, phage integrase family (NCBI) 46, 49
GSU0517 GSU0517 conserved domain protein (NCBI) 60, 236
GSU0537 GSU0537 sensory box/GGDEF family protein (VIMSS) 236, 290
GSU0724 GSU0724 conserved hypothetical protein (NCBI) 49, 234
GSU0730 GSU0730 hypothetical protein (VIMSS) 63, 236
GSU0832 GSU0832 lipoprotein, putative (VIMSS) 71, 236
GSU0838 GSU0838 hypothetical protein (VIMSS) 155, 236
GSU0918 GSU0918 S-adenosylmethionine synthetase family protein (NCBI) 49, 240
GSU1038 GSU1038 sensory box histidine kinase/response regulator (VIMSS) 236, 269
GSU1096 pstB phosphate ABC transporter, ATP-binding protein (NCBI) 16, 236
GSU1102 regX3 DNA-binding response regulator (NCBI) 115, 236
GSU1417 GSU1417 response regulator (VIMSS) 78, 236
GSU1419 GSU1419 transcriptional regulator, Cro/CI family (VIMSS) 219, 236
GSU1676 GSU1676 hypothetical protein (VIMSS) 96, 236
GSU1697 GSU1697 membrane protein, putative (VIMSS) 236, 291
GSU1743 GSU1743 lipoprotein, putative (VIMSS) 166, 236
GSU1745 GSU1745 OmpA domain protein (VIMSS) 236, 265
GSU1858 GSU1858 IPT/TIG domain protein (VIMSS) 155, 236
GSU2344 GSU2344 NADH-ubiquinone/plastoquinone family protein (VIMSS) 49, 133
GSU2348 GSU2348 conserved hypothetical protein (VIMSS) 49, 97
GSU2350 GSU2350 potassium uptake protein, Kup system (VIMSS) 49, 281
GSU2351 GSU2351 cation-transport ATPase, E1-E2 family (VIMSS) 49, 237
GSU2354 GSU2354 transcriptional regulator, IclR family (VIMSS) 49, 236
GSU2412 GSU2412 hypothetical protein (NCBI) 49, 310
GSU2431 GSU2431 membrane protein, putative (NCBI) 40, 49
GSU2433 GSU2433 ATP-dependent protease, putative (VIMSS) 20, 49
GSU2475 GSU2475 sigma-54 dependent transcriptional regulator (NCBI) 40, 49
GSU2482 kdpC potassium-transporting ATPase, C subunit (NCBI) 49, 97
GSU2483 kdpD sensor histidine kinase KdpD (NCBI) 20, 49
GSU2650 GSU2650 amino acid ABC transporter, permease protein, putative (VIMSS) 49, 237
GSU2682 GSU2682 conserved hypothetical protein (VIMSS) 49, 65
GSU2686 GSU2686 ABC transporter, ATP-binding protein (VIMSS) 49, 327
GSU2744 GSU2744 major facilitator family transporter (VIMSS) 49, 304
GSU2745 GSU2745 ATPase, AAA family (VIMSS) 49, 304
GSU3026 GSU3026 flagellar protein FlbD, putative (VIMSS) 110, 236
GSU3091 cvpA CvpA family protein (NCBI) 16, 236
GSU3124 GSU3124 iron-sulfur cluster-binding protein (VIMSS) 137, 236
GSU3239 cafA ribonuclease G (NCBI) 96, 236
GSU3412 GSU3412 hypothetical protein (VIMSS) 49, 140
GSU3416 GSU3416 hypothetical protein (VIMSS) 115, 236
GSU3446 GSU3446 thioredoxin family protein, selenocysteine-containing (NCBI) 40, 49
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 GSU2354
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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