Organism : Geobacter sulfurreducens | Module List :
GSU0308 hypD

hydrogenase expression/formation protein HypD (NCBI)

CircVis
Functional Annotations (3)
Function System
Hydrogenase maturation factor cog/ cog
metal ion binding go/ molecular_function
hypD tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0308
(Mouseover regulator name to see its description)

GSU0308 is regulated by 13 influences and regulates 0 modules.
Regulators for GSU0308 hypD (13)
Regulator Module Operator
GSU0300 322 tf
GSU0359 322 tf
GSU0473 322 tf
GSU0551 322 tf
GSU0735 322 tf
GSU2506 322 tf
GSU2587 322 tf
GSU3087 322 tf
GSU3217 322 tf
GSU0770 44 tf
GSU1495 44 tf
GSU1569 44 tf
GSU2177 44 tf

Warning: GSU0308 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
2248 1.60e-01 GtTTCcCTcCacCgg
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2249 3.50e+01 tCacccTtcGcAaAAACgGtGaaa
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2800 7.00e+02 CTCCTc
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2801 9.80e+03 ccGatt.TC.ctGtttactgta
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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 GSU0308

GSU0308 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Hydrogenase maturation factor cog/ cog
metal ion binding go/ molecular_function
hypD tigr/ tigrfam
Module neighborhood information for GSU0308

GSU0308 has total of 30 gene neighbors in modules 44, 322
Gene neighbors (30)
Gene Common Name Description Module membership
GSU0230 pilT-2 twitching motility protein PilT (NCBI) 308, 322
GSU0234 GSU0234 transporter, FNT family (VIMSS) 224, 322
GSU0305 hypB hydrogenase accessory protein HypB (NCBI) 42, 44
GSU0308 hypD hydrogenase expression/formation protein HypD (NCBI) 44, 322
GSU0360 GSU0360 OmpA domain protein (VIMSS) 44, 210
GSU0393 GSU0393 hypothetical protein (VIMSS) 44, 137
GSU0412 GSU0412 flagellar assembly protein fliH, putative (VIMSS) 186, 322
GSU0502 GSU0502 lipoprotein, putative (VIMSS) 130, 322
GSU0573 GSU0573 alcohol dehydrogenase, zinc-containing (VIMSS) 295, 322
GSU0585 GSU0585 fumarylacetoacetate hydrolase family protein (VIMSS) 44, 99
GSU0588 thiG thiamine biosynthesis protein ThiG (NCBI) 44, 99
GSU0814 GSU0814 outer membrane efflux protein, putative (VIMSS) 44, 210
GSU0876 GSU0876 diacylglycerol kinase catalytic domain protein (NCBI) 89, 322
GSU0898 recQ ATP-dependent DNA helicase RecQ (NCBI) 44, 133
GSU1616 dinP ImpB/MucB/SamB family protein (NCBI) 269, 322
GSU2096 GSU2096 iron-sulfur cluster-binding protein (VIMSS) 113, 322
GSU2158 norQ cobS protein, putative (NCBI) 1, 322
GSU2375 GSU2375 None 126, 322
GSU2461 GSU2461 hypothetical protein (VIMSS) 44, 108
GSU2564 GSU2564 hypothetical protein (VIMSS) 44, 208
GSU2591 GSU2591 ISGsu5, transposase (VIMSS) 322, 337
GSU2974 GSU2974 methylenetetrahydrofolate reductase family protein (VIMSS) 224, 322
GSU3028 motB chemotaxis MotB protein (NCBI) 322, 337
GSU3166 GSU3166 conserved hypothetical protein (VIMSS) 130, 322
GSU3280 GSU3280 thioredoxin-related protein (NCBI) 44, 203
GSU3281 trx thioredoxin (NCBI) 44, 60
GSU3283 GSU3283 cytochrome c biogenesis protein, CcmF/CcyK/CcsA family (VIMSS) 44, 89
GSU3284 hemA glutamyl-tRNA reductase (NCBI) 44, 60
GSU3285 hemC porphobilinogen deaminase (NCBI) 44, 263
GSU3289 GSU3289 conserved hypothetical protein (VIMSS) 44, 60
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 GSU0308
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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