Organism : Geobacter sulfurreducens | Module List :
GSU0013

transcriptional regulator, MarR family (VIMSS)

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators cog/ cog
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 GSU0013
(Mouseover regulator name to see its description)

GSU0013 is regulated by 25 influences and regulates 29 modules.
Regulators for GSU0013 (25)
Regulator Module Operator
GSU0013 229 tf
GSU0175 229 tf
GSU0266 229 tf
GSU1687 229 tf
GSU1727 229 tf
GSU1989 229 tf
GSU1992 229 tf
GSU2237 229 tf
GSU2581 229 tf
GSU3087 229 tf
GSU3387 229 tf
GSU3421 229 tf
GSU0013 134 tf
GSU0031 134 tf
GSU0178 134 tf
GSU0721 134 tf
GSU1013 134 tf
GSU1218 134 tf
GSU1495 134 tf
GSU1525 134 tf
GSU2149 134 tf
GSU2581 134 tf
GSU2666 134 tf
GSU2787 134 tf
GSU3229 134 tf

Warning: GSU0013 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
2428 5.90e-01 aAAtGttcggAtAccaAaAtaTTA
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2429 3.20e+00 ActgACagcGGGGcAaatTaCcaT
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2618 1.80e-01 tGCGaATgg.TtA.TATTaT.GTG
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2619 1.30e+03 CcAGcacatA.TtTT
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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 GSU0013

GSU0013 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators cog/ cog
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 GSU0013

GSU0013 has total of 34 gene neighbors in modules 134, 229
Gene neighbors (34)
Gene Common Name Description Module membership
GSU0012 hemG protoporphyrinogen oxidase (VIMSS) 16, 134
GSU0013 GSU0013 transcriptional regulator, MarR family (VIMSS) 134, 229
GSU0014 dnaJ phage prohead protease, HK97 family/dnaJ domain protein (NCBI) 16, 134
GSU0035 GSU0035 2',5' RNA ligase, putative (NCBI) 229, 294
GSU0101 GSU0101 ABC transporter, ATP-binding/permease protein (VIMSS) 166, 229
GSU0128 priA primosomal protein n` (NCBI) 2, 134
GSU0394 GSU0394 AcrB/AcrD/AcrF family protein (VIMSS) 14, 229
GSU0396 GSU0396 conserved hypothetical protein (VIMSS) 96, 229
GSU0434 GSU0434 conserved hypothetical protein (VIMSS) 229, 318
GSU0448 GSU0448 hydrolase, putative (VIMSS) 73, 134
GSU0543 GSU0543 outer membrane lipoprotein, Slp family, putative (VIMSS) 229, 252
GSU0544 GSU0544 conserved hypothetical protein (NCBI) 229, 252
GSU0746 GSU0746 cytochrome p460, putative (VIMSS) 134, 177
GSU0764 GSU0764 hypothetical protein (VIMSS) 229, 337
GSU1001 GSU1001 hypothetical protein (VIMSS) 76, 229
GSU1062 GSU1062 cytochrome c, putative (NCBI) 165, 229
GSU1063 GSU1063 hypothetical protein (VIMSS) 229, 251
GSU1430 GSU1430 hypothetical protein (VIMSS) 53, 229
GSU1431 GSU1431 conserved hypothetical protein (VIMSS) 118, 229
GSU1447 GSU1447 hypothetical protein (VIMSS) 229, 251
GSU1556 GSU1556 hypothetical protein (VIMSS) 86, 229
GSU1796 GSU1796 DHH family protein (VIMSS) 200, 229
GSU1943 GSU1943 hypothetical protein (VIMSS) 229, 241
GSU2174 GSU2174 conserved hypothetical protein (VIMSS) 229, 252
GSU2424 GSU2424 hypothetical protein (VIMSS) 85, 134
GSU2662 GSU2662 membrane protein, putative (VIMSS) 2, 134
GSU2690 GSU2690 conserved hypothetical protein (VIMSS) 109, 229
GSU2801 GSU2801 cytochrome c family protein (NCBI) 229, 259
GSU2812 GSU2812 glutaredoxin family protein (VIMSS) 134, 195
GSU3020 GSU3020 hexapeptide transferase family protein (VIMSS) 200, 229
GSU3229 GSU3229 DNA-binding response regulator, LuxR family (VIMSS) 134, 259
GSU3230 GSU3230 sensory box histidine kinase (VIMSS) 134, 246
GSU3248 GSU3248 hypothetical protein (VIMSS) 63, 134
GSU3341 GSU3341 hypothetical protein (NCBI) 134, 177
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 GSU0013
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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