Organism : Geobacter sulfurreducens | Module List :
GSU0122

nickel-dependent hydrogenase, large subunit (VIMSS)

CircVis
Functional Annotations (5)
Function System
Ni,Fe-hydrogenase I large subunit cog/ cog
electron transport go/ biological_process
ferredoxin hydrogenase activity go/ molecular_function
nickel ion binding go/ molecular_function
hydrogenase (acceptor) activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0122
(Mouseover regulator name to see its description)

GSU0122 is regulated by 17 influences and regulates 0 modules.
Regulators for GSU0122 (17)
Regulator Module Operator
GSU0266 21 tf
GSU0372 21 tf
GSU0581 21 tf
GSU1003 21 tf
GSU1525 21 tf
GSU1934 21 tf
GSU2202 21 tf
GSU2831 21 tf
GSU0205 157 tf
GSU1617 157 tf
GSU2741 157 tf
GSU2817 157 tf
GSU2964 157 tf
GSU3045 157 tf
GSU3109 157 tf
GSU3324 157 tf
GSU3418 157 tf

Warning: GSU0122 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
2202 7.90e-08 ttAACGttTTaT.ATt
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2203 1.50e-02 GAATGtTAAtatAaaTTtAgAcat
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2474 5.80e-01 aaaaAaccactaaaaaatAAcaTt
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2475 1.60e+01 gag.AcC.tttaCgGGca.At
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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 GSU0122

GSU0122 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Ni,Fe-hydrogenase I large subunit cog/ cog
electron transport go/ biological_process
ferredoxin hydrogenase activity go/ molecular_function
nickel ion binding go/ molecular_function
hydrogenase (acceptor) activity go/ molecular_function
Module neighborhood information for GSU0122

GSU0122 has total of 42 gene neighbors in modules 21, 157
Gene neighbors (42)
Gene Common Name Description Module membership
GSU0057 GSU0057 CRISPR-associated protein Cas1/Cas4 (NCBI) 157, 195
GSU0058 GSU0058 CRISPR-associated protein Cas2, putative (NCBI) 157, 195
GSU0122 GSU0122 nickel-dependent hydrogenase, large subunit (VIMSS) 21, 157
GSU0132 GSU0132 conserved hypothetical protein (VIMSS) 155, 157
GSU0178 GSU0178 conserved hypothetical protein (VIMSS) 157, 202
GSU0218 GSU0218 conserved hypothetical protein (VIMSS) 21, 266
GSU0265 GSU0265 membrane protein, putative (VIMSS) 21, 186
GSU0395 GSU0395 conserved hypothetical protein (VIMSS) 94, 157
GSU0428 GSU0428 lipoprotein, putative (VIMSS) 21, 278
GSU0433 GSU0433 clpB protein, putative (NCBI) 21, 96
GSU0583 GSU0583 methyl-accepting chemotaxis protein (VIMSS) 100, 157
GSU0692 GSU0692 carbohydrate kinase, PfkB family (VIMSS) 9, 157
GSU0693 GSU0693 sensory box histidine kinase (VIMSS) 103, 157
GSU0760 GSU0760 hypothetical protein (VIMSS) 151, 157
GSU0837 GSU0837 response regulator (VIMSS) 21, 155
GSU0848 GSU0848 ferredoxin family protein, putative (VIMSS) 21, 189
GSU0849 GSU0849 conserved hypothetical protein (VIMSS) 21, 157
GSU0942 suhB inositol-1-monophosphatase (NCBI) 157, 193
GSU1015 GSU1015 hypothetical protein (VIMSS) 21, 189
GSU1036 GSU1036 sensor histidine kinase (VIMSS) 53, 157
GSU1049 GSU1049 conserved hypothetical protein (NCBI) 21, 272
GSU1050 GSU1050 sensory box histidine kinase (VIMSS) 21, 272
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
GSU1066 GSU1066 hypothetical protein (NCBI) 4, 157
GSU1185 GSU1185 conserved hypothetical protein (VIMSS) 41, 157
GSU1299 cheW purine-binding chemotaxis protein CheW (NCBI) 59, 157
GSU1415 GSU1415 response regulator (VIMSS) 21, 157
GSU1685 GSU1685 HD domain protein (NCBI) 21, 38
GSU2349 GSU2349 hypothetical protein (VIMSS) 21, 45
GSU2512 GSU2512 hypothetical protein (VIMSS) 21, 180
GSU2562 sixA phosphohistidine phosphatase SixA (NCBI) 140, 157
GSU2689 GSU2689 hypothetical protein (VIMSS) 113, 157
GSU2791 GSU2791 hypothetical protein (RefSeq) 65, 157
GSU3012 GSU3012 hypothetical protein (VIMSS) 38, 157
GSU3324 GSU3324 transcriptional regulator, Cro/CI family (VIMSS) 13, 157
GSU3345 GSU3345 hypothetical protein (VIMSS) 113, 157
GSU3414 GSU3414 hypothetical protein (VIMSS) 41, 157
GSU3415 GSU3415 radical SAM domain protein/B12 binding domain protein (NCBI) 21, 157
GSU3417 GSU3417 dioxygenase, putative (VIMSS) 21, 59
GSU3418 GSU3418 sigma-54 dependent DNA-binding response regulator (VIMSS) 21, 274
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 GSU0122
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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