Organism : Geobacter sulfurreducens | Module List :
GSU1617 lexA-2

LexA repressor (NCBI)

CircVis
Functional Annotations (6)
Function System
SOS-response transcriptional repressors (RecA-mediated autopeptidases) cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
proteolysis go/ biological_process
repressor LexA activity go/ molecular_function
lexA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1617
(Mouseover regulator name to see its description)

GSU1617 is regulated by 15 influences and regulates 15 modules.
Regulators for GSU1617 lexA-2 (15)
Regulator Module Operator
GSU0063 45 tf
GSU0366 45 tf
GSU1483 45 tf
GSU1617 45 tf
GSU2625 45 tf
GSU3298 45 tf
GSU3387 45 tf
GSU3396 45 tf
GSU0041 216 tf
GSU0178 216 tf
GSU0366 216 tf
GSU1495 216 tf
GSU2809 216 tf
GSU2964 216 tf
GSU3127 216 tf

Warning: GSU1617 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
2250 2.00e+03 CC.ggca..cGGGatagaggAgaT
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2251 1.40e+04 caatatCaacCAACAagGaggca
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2592 4.10e+02 TcAT.AAA
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2593 5.80e+02 tGacaTaTaT..a.cAAatt
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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 GSU1617

GSU1617 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
SOS-response transcriptional repressors (RecA-mediated autopeptidases) cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
proteolysis go/ biological_process
repressor LexA activity go/ molecular_function
lexA tigr/ tigrfam
Module neighborhood information for GSU1617

GSU1617 has total of 40 gene neighbors in modules 45, 216
Gene neighbors (40)
Gene Common Name Description Module membership
GSU0071 GSU0071 hypothetical protein (VIMSS) 177, 216
GSU0103 GSU0103 sensory box histidine kinase (VIMSS) 200, 216
GSU0172 dnrV conserved hypothetical protein (NCBI) 86, 216
GSU0184 b2690 HAD-superfamily hydrolase, subfamily IA, variant 1 (NCBI) 45, 234
GSU0279 GSU0279 cadherin domain/calx-beta domain protein (NCBI) 45, 253
GSU0366 GSU0366 transcriptional regulator, putative (VIMSS) 45, 280
GSU0391 GSU0391 Outer membrane efflux family protein (VIMSS) 216, 230
GSU0401 GSU0401 methyl-accepting chemotaxis protein, putative (VIMSS) 216, 235
GSU0403 cheY-1 chemotaxis protein CheY (NCBI) 216, 235
GSU0596 GSU0596 response regulator (NCBI) 45, 86
GSU0597 GSU0597 hypothetical protein (VIMSS) 45, 59
GSU0683 GSU0683 methyl-accepting chemotaxis protein, putative (VIMSS) 45, 79
GSU0752 GSU0752 transporter, putative (VIMSS) 216, 257
GSU0891 GSU0891 subtilase domain protein (NCBI) 45, 218
GSU0917 GSU0917 conserved hypothetical protein (VIMSS) 45, 294
GSU1303 GSU1303 methyl-accepting chemotaxis protein (VIMSS) 45, 234
GSU1532 nrd conserved domain protein (NCBI) 45, 165
GSU1533 recC exodeoxyribonuclease V, gamma subunit (NCBI) 45, 266
GSU1534 recB exodeoxyribonuclease V, beta subunit (NCBI) 15, 45
GSU1617 lexA-2 LexA repressor (NCBI) 45, 216
GSU1711 GSU1711 integrative genetic element Gsu5, resolvase (VIMSS) 45, 104
GSU1995 GSU1995 hypothetical protein (VIMSS) 193, 216
GSU2349 GSU2349 hypothetical protein (VIMSS) 21, 45
GSU2473 vapB virulence associated protein B (NCBI) 193, 216
GSU2491 GSU2491 major facilitator family transporter (VIMSS) 216, 331
GSU2530 GSU2530 GTPase YjeQ (NCBI) 45, 141
GSU2560 GSU2560 hypothetical protein (NCBI) 140, 216
GSU2663 GSU2663 lipoprotein, putative (VIMSS) 216, 273
GSU2809 GSU2809 transcriptional regulator, Fur family (VIMSS) 193, 216
GSU2934 GSU2934 cytochrome c family protein (NCBI) 45, 266
GSU2935 GSU2935 cytochrome c family protein (NCBI) 45, 133
GSU2968 GSU2968 hypothetical protein (VIMSS) 85, 216
GSU2988 GSU2988 conserved hypothetical protein (VIMSS) 45, 193
GSU3032 GSU3032 hypothetical protein (VIMSS) 45, 234
GSU3036 fliS flagellar protein FliS (NCBI) 150, 216
GSU3139 GSU3139 conserved hypothetical protein (VIMSS) 53, 216
GSU3141 GSU3141 hypothetical protein (VIMSS) 4, 216
GSU3142 GSU3142 phospho-2-dehydro-3-deoxyheptonate aldolase (NCBI) 4, 216
GSU3461 GSU3461 thioesterase family protein (NCBI) 216, 235
GSU3462 GSU3462 lipoprotein, putative (VIMSS) 187, 216
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 GSU1617
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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