Organism : Geobacter sulfurreducens | Module List :
GSU3109

transcriptional regulator, IclR family (NCBI)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3109
(Mouseover regulator name to see its description)

GSU3109 is regulated by 18 influences and regulates 11 modules.
Regulators for GSU3109 (18)
Regulator Module Operator
GSU0366 133 tf
GSU1495 133 tf
GSU1586 133 tf
GSU1653 133 tf
GSU1934 133 tf
GSU2033 133 tf
GSU2149 133 tf
GSU2753 133 tf
GSU2941 133 tf
GSU3109 133 tf
GSU3396 133 tf
GSU1320 99 tf
GSU1495 99 tf
GSU1569 99 tf
GSU2033 99 tf
GSU2113 99 tf
GSU2520 99 tf
GSU3109 99 tf

Warning: GSU3109 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
2358 6.50e+01 GtTcCt.CGGGctTTtTtgtTTT
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2359 8.60e+02 tc.ccctGgCggcgGcaAgcg
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2426 1.20e+00 tataatac.accAgA.ta.ggcca
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2427 1.00e+01 TttgTc.tatCAtcCGtatt
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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 GSU3109

GSU3109 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Transcriptional regulator cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for GSU3109

GSU3109 has total of 50 gene neighbors in modules 99, 133
Gene neighbors (50)
Gene Common Name Description Module membership
GSU0222 GSU0222 cytochrome c oxidase, subunit II (VIMSS) 99, 257
GSU0283 GSU0283 sensor histidine kinase (VIMSS) 99, 203
GSU0287 GSU0287 HD domain protein (VIMSS) 49, 133
GSU0318 GSU0318 peptidase, M48 family (NCBI) 99, 336
GSU0437 ubiD 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (NCBI) 99, 235
GSU0454 GSU0454 conserved hypothetical protein (VIMSS) 99, 160
GSU0493 ndh NADH respiratory dehydrogenase (Regina ONeil) 133, 235
GSU0494 GSU0494 iron-sulfur cluster-binding protein (VIMSS) 133, 336
GSU0519 GSU0519 conserved hypothetical protein (VIMSS) 99, 225
GSU0522 rhlB ATP-dependent RNA helicase RhlB (NCBI) 81, 133
GSU0575 cstA carbon starvation protein A (NCBI) 99, 127
GSU0585 GSU0585 fumarylacetoacetate hydrolase family protein (VIMSS) 44, 99
GSU0586 GSU0586 radical SAM protein, TIGR01212 family (NCBI) 99, 133
GSU0588 thiG thiamine biosynthesis protein ThiG (NCBI) 44, 99
GSU0589 GSU0589 conserved hypothetical protein (VIMSS) 60, 99
GSU0605 thiD thiamine-phosphate pyrophosphorylase/phosphomethylpyrimidine kinase (NCBI) 99, 287
GSU0768 GSU0768 AzlC family protein (VIMSS) 99, 122
GSU0806 citG ATP:dephospho-CoA triphosphoribosyl transferase (NCBI) 95, 133
GSU0898 recQ ATP-dependent DNA helicase RecQ (NCBI) 44, 133
GSU0921 rne ribonuclease, Rne/Rng family protein (NCBI) 20, 99
GSU0923 loN-1 ATP-dependent protease La (NCBI) 20, 133
GSU0924 GSU0924 ABC transporter, permease protein, putative (VIMSS) 20, 133
GSU1056 GSU1056 conserved hypothetical protein TIGR00149 (VIMSS) 21, 133
GSU1057 GSU1057 hypothetical protein (VIMSS) 21, 133
GSU1058 sucC succinyl-CoA synthase, beta subunit (NCBI) 21, 133
GSU1325 GSU1325 hypothetical protein (NCBI) 99, 142
GSU1553 GSU1553 conserved hypothetical protein (VIMSS) 99, 220
GSU1696 GSU1696 MoxR family protein (VIMSS) 65, 133
GSU1770 GSU1770 hypothetical protein (VIMSS) 133, 253
GSU1998 GSU1998 transporter, putative (VIMSS) 8, 99
GSU2002 GSU2002 conserved domain protein (NCBI) 99, 127
GSU2300 GSU2300 hypothetical protein (VIMSS) 99, 287
GSU2344 GSU2344 NADH-ubiquinone/plastoquinone family protein (VIMSS) 49, 133
GSU2492 GSU2492 sensory box histidine kinase (VIMSS) 99, 160
GSU2685 GSU2685 membrane protein, putative (VIMSS) 99, 107
GSU2701 GSU2701 ABC transporter, permease protein (VIMSS) 99, 133
GSU2713 GSU2713 conserved hypothetical protein (VIMSS) 4, 133
GSU2726 GSU2726 hypothetical protein (VIMSS) 133, 237
GSU2813 ccpA-2 cytochrome c551 peroxidase (NCBI) 65, 99
GSU2827 GSU2827 conserved hypothetical protein (VIMSS) 133, 235
GSU2935 GSU2935 cytochrome c family protein (NCBI) 45, 133
GSU2978 GSU2978 hypothetical protein (VIMSS) 133, 140
GSU2979 folK 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase (NCBI) 133, 273
GSU3058 GSU3058 dihydroorotate dehydrogenase, electron transfer subunit, putative (NCBI) 99, 145
GSU3095 hisF imidazoleglycerol phosphate synthase, cyclase subunit (NCBI) 53, 99
GSU3109 GSU3109 transcriptional regulator, IclR family (NCBI) 99, 133
GSU3161 msrA peptide methionine sulfoxide reductase (NCBI) 60, 99
GSU3332 GSU3332 cytochrome c family protein, putative (NCBI) 133, 256
GSU3347 GSU3347 peptidase, U32 family (NCBI) 99, 127
GSU3360 GSU3360 peptidase, M16 family (NCBI) 99, 127
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 GSU3109
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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