Organism : Geobacter sulfurreducens | Module List :
GSU0429

conserved hypothetical protein (VIMSS)

CircVis
Functional Annotations (2)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
VI_chp_4 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0429
(Mouseover regulator name to see its description)

GSU0429 is regulated by 17 influences and regulates 0 modules.
Regulators for GSU0429 (17)
Regulator Module Operator
GSU0187 275 tf
GSU0682 275 tf
GSU0735 275 tf
GSU0776 275 tf
GSU1320 275 tf
GSU1495 275 tf
GSU1831 275 tf
GSU2033 275 tf
GSU2506 275 tf
GSU3324 275 tf
GSU0254 135 tf
GSU0551 135 tf
GSU0735 135 tf
GSU1072 135 tf
GSU2716 135 tf
GSU3108 135 tf
GSU3217 135 tf

Warning: GSU0429 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
2430 9.40e-05 TtttgaaaAatagtt.TAAaGT.T
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2431 2.40e+02 gTcaAtaAAaatAaAACAcc.ttT
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2710 8.30e-03 AAATtgTAaTaacagaAgAtTAAT
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2711 4.40e+01 AcAGcAAc.cCGtaAgATAa
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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 GSU0429

GSU0429 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
VI_chp_4 tigr/ tigrfam
Module neighborhood information for GSU0429

GSU0429 has total of 37 gene neighbors in modules 135, 275
Gene neighbors (37)
Gene Common Name Description Module membership
GSU0073 GSU0073 outer membrane protein, putative (VIMSS) 160, 275
GSU0138 prfC peptide chain release factor 3 (NCBI) 140, 275
GSU0426 flhB flagellar biosynthetic protein FlhB (NCBI) 82, 275
GSU0429 GSU0429 conserved hypothetical protein (VIMSS) 135, 275
GSU0599 GSU0599 sensor histidine kinase (VIMSS) 9, 275
GSU0601 GSU0601 alpha amylase family protein (VIMSS) 23, 275
GSU0602 GSU0602 conserved hypothetical protein (VIMSS) 140, 275
GSU0682 GSU0682 DNA-binding response regulator, LuxR family (VIMSS) 275, 299
GSU0706 GSU0706 major facilitator family transporter (VIMSS) 234, 275
GSU1072 GSU1072 transcriptional regulator, IclR family (VIMSS) 57, 135
GSU1109 GSU1109 hypothetical protein (VIMSS) 275, 281
GSU1153 GSU1153 outer membrane protein, OMP85 family (NCBI) 275, 299
GSU1158 sodA superoxide dismutase (NCBI) 275, 310
GSU1162 GSU1162 ABC transporter, ATP-binding protein (VIMSS) 275, 310
GSU1414 GSU1414 sensory box histidine kinase/response regulator (VIMSS) 53, 275
GSU2005 GSU2005 branched-chain amino acid ABC transporter, periplasmic amino acid-binding protein, putative (NCBI) 135, 142
GSU2006 GSU2006 branched-chain amino acid ABC transporter, permease protein (NCBI) 135, 142
GSU2007 GSU2007 branched-chain amino acid ABC transporter, permease protein (NCBI) 135, 142
GSU2008 GSU2008 branched-chain amino acid ABC transporter, ATP-binding protein (NCBI) 135, 142
GSU2009 GSU2009 branched-chain amino acid ABC transporter, ATP-binding protein (VIMSS) 135, 142
GSU2010 GSU2010 CBS domain protein (VIMSS) 135, 142
GSU2132 GSU2132 hypothetical protein (VIMSS) 113, 275
GSU2155 GSU2155 hypothetical protein (VIMSS) 70, 135
GSU2355 GSU2355 hypothetical protein (VIMSS) 6, 135
GSU2417 GSU2417 hypothetical protein (VIMSS) 57, 135
GSU2419 GSU2419 nickel-dependent hydrogenase, large subunit (VIMSS) 78, 135
GSU2557 GSU2557 polysaccharide deacetylase family protein (NCBI) 122, 135
GSU2652 GSU2652 methyl-accepting chemotaxis protein (VIMSS) 128, 275
GSU2768 GSU2768 hypothetical protein (VIMSS) 122, 135
GSU2826 GSU2826 membrane protein, putative (VIMSS) 140, 275
GSU2898 GSU2898 high-molecular-weight cytochrome c (NCBI) 117, 275
GSU2899 GSU2899 high-molecular-weight cytochrome c (NCBI) 166, 275
GSU3016 GSU3016 hypothetical protein (VIMSS) 122, 135
GSU3120 GSU3120 conserved hypothetical protein (VIMSS) 122, 135
GSU3218 GSU3218 cytochrome c family protein (NCBI) 135, 155
GSU3355 GSU3355 hypothetical protein (VIMSS) 135, 246
GSU3434 nuoI-2 NADH dehydrogenase I, I subunit (NCBI) 160, 275
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 GSU0429
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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