Organism : Geobacter sulfurreducens | Module List :
GSU0306 hypF

hydrogenase maturation protein HypF (NCBI)

CircVis
Functional Annotations (5)
Function System
Hydrogenase maturation factor cog/ cog
acylphosphatase activity go/ molecular_function
zinc ion binding go/ molecular_function
transcription regulator activity go/ molecular_function
hypF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0306
(Mouseover regulator name to see its description)

GSU0306 is regulated by 20 influences and regulates 0 modules.
Regulators for GSU0306 hypF (20)
Regulator Module Operator
GSU0372 171 tf
GSU0598 171 tf
GSU0735 171 tf
GSU1345 171 tf
GSU1687 171 tf
GSU2033 171 tf
GSU2362 171 tf
GSU2524 171 tf
GSU0300 94 tf
GSU0399 94 tf
GSU0598 94 tf
GSU0736 94 tf
GSU0963 94 tf
GSU1345 94 tf
GSU1410 94 tf
GSU1940 94 tf
GSU2354 94 tf
GSU2698 94 tf
GSU2915 94 tf
GSU3292 94 tf

Warning: GSU0306 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
2348 1.60e+04 GagAtaaGcACAaA
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2349 1.90e+04 cttttccgCCaggaGCGcCgggCg
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2502 1.10e+04 GtCa.aTGG
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2503 1.90e+03 tTcCTgt..cAtTg
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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 GSU0306

GSU0306 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Hydrogenase maturation factor cog/ cog
acylphosphatase activity go/ molecular_function
zinc ion binding go/ molecular_function
transcription regulator activity go/ molecular_function
hypF tigr/ tigrfam
Module neighborhood information for GSU0306

GSU0306 has total of 21 gene neighbors in modules 94, 171
Gene neighbors (21)
Gene Common Name Description Module membership
GSU0306 hypF hydrogenase maturation protein HypF (NCBI) 94, 171
GSU0309 hypE hydrogenase expression/formation protein hype (VIMSS) 94, 205
GSU0313 GSU0313 DnaJ domain protein (VIMSS) 25, 171
GSU0395 GSU0395 conserved hypothetical protein (VIMSS) 94, 157
GSU0399 GSU0399 transcriptional regulator, ArsR family (VIMSS) 94, 336
GSU0499 GSU0499 M23/M37 peptidase domain protein (VIMSS) 77, 94
GSU0772 GSU0772 NADPH-dependent FMN reductase domain protein (NCBI) 94, 115
GSU1117 GSU1117 response regulator (VIMSS) 94, 264
GSU1119 GSU1119 sensor histidine kinase/response regulator (VIMSS) 94, 264
GSU1157 GSU1157 conserved hypothetical protein (VIMSS) 25, 171
GSU1384 cas3 CRISPR-associated helicase Cas3 (NCBI) 94, 130
GSU1404 GSU1404 radical SAM domain protein (NCBI) 171, 193
GSU2207 GSU2207 DNA polymerase III, delta subunit, putative (NCBI) 77, 94
GSU2208 GSU2208 lipoprotein, putative (VIMSS) 77, 94
GSU2217 GSU2217 response regulator (VIMSS) 77, 94
GSU2338 GSU2338 Na+/H+ antiporter component (VIMSS) 155, 171
GSU2339 GSU2339 monovalent cation/proton antiporter, MrpF/PhaF family (NCBI) 94, 289
GSU2648 GSU2648 conserved hypothetical protein (VIMSS) 54, 171
GSU3067 murB UDP-N-acetylenolpyruvoylglucosamine reductase (NCBI) 94, 264
GSU3068 murC UDP-N-acetylmuramate--alanine ligase (NCBI) 94, 264
GSU3427 GSU3427 lipoprotein, putative (VIMSS) 42, 94
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 GSU0306
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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