Organism : Geobacter sulfurreducens | Module List :
GSU0551

conserved hypothetical protein (VIMSS)

CircVis
Functional Annotations (1)
Function System
Predicted transcriptional regulator cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0551
(Mouseover regulator name to see its description)

GSU0551 is regulated by 11 influences and regulates 18 modules.
Regulators for GSU0551 (11)
Regulator Module Operator
GSU0551 173 tf
GSU0735 173 tf
GSU0770 173 tf
GSU2524 173 tf
GSU3041 173 tf
GSU3370 173 tf
GSU0359 335 tf
GSU0551 335 tf
GSU0770 335 tf
GSU1940 335 tf
GSU3108 335 tf

Warning: GSU0551 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
2506 3.90e+02 TgtTtTTCgC
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2507 1.40e+04 AaTcGaGtaataTtGTCTG
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2826 3.70e+00 CaAaAAAa
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2827 3.50e+03 TcaTTATGatc.cCAt..CC
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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 GSU0551

GSU0551 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted transcriptional regulator cog/ cog
Module neighborhood information for GSU0551

GSU0551 has total of 37 gene neighbors in modules 173, 335
Gene neighbors (37)
Gene Common Name Description Module membership
GSU0094 dnaX DNA polymerase III, gamma and tau subunits (NCBI) 173, 318
GSU0102 selB selenocysteine-specific translation elongation factor (NCBI) 335, 338
GSU0106 GSU0106 soj protein (VIMSS) 286, 335
GSU0115 pdxA pyridoxal phosphate biosynthetic protein PdxA (NCBI) 200, 335
GSU0176 GSU0176 conserved hypothetical protein (VIMSS) 173, 335
GSU0330 GSU0330 general secretion pathway protein C, putative (NCBI) 173, 189
GSU0525 dtd D-tyrosyl-tRNA(Tyr) deacylase (NCBI) 84, 173
GSU0551 GSU0551 conserved hypothetical protein (VIMSS) 173, 335
GSU0560 GSU0560 hypothetical protein (VIMSS) 179, 335
GSU0628 GSU0628 conserved domain protein (VIMSS) 173, 323
GSU0669 GSU0669 hypothetical protein (VIMSS) 173, 225
GSU0694 GSU0694 HAD-superfamily hydrolase, subfamily IA, variant 1 (NCBI) 165, 173
GSU0795 GSU0795 Rhodanese-like domain protein (VIMSS) 173, 252
GSU0887 GSU0887 conserved hypothetical protein (VIMSS) 144, 335
GSU0930 GSU0930 sulfur transferase, putative, selenocysteine-containing (NCBI) 84, 173
GSU0943 GSU0943 hypothetical protein (VIMSS) 304, 335
GSU1006 GSU1006 hypothetical protein (VIMSS) 265, 335
GSU1065 GSU1065 hypothetical protein (VIMSS) 173, 189
GSU1191 GSU1191 hypothetical protein (VIMSS) 335, 338
GSU1229 GSU1229 lipoprotein, putative (VIMSS) 173, 213
GSU1355 GSU1355 ISGsu7, transposase OrfA (VIMSS) 335, 341
GSU1356 GSU1356 ISGsu7, transposase OrfB (VIMSS) 47, 335
GSU1475 GSU1475 RNA methyltransferase, TrmH family, group 1 (VIMSS) 124, 335
GSU1561 GSU1561 penicillin-binding protein, 1A family (VIMSS) 84, 173
GSU1609 GSU1609 outer membrane efflux protein (VIMSS) 159, 335
GSU1820 GSU1820 protein-P-II uridylyltransferase, putative (VIMSS) 163, 335
GSU1870 GSU1870 GGDEF domain protein (VIMSS) 183, 335
GSU1940 GSU1940 sigma-54 dependent DNA-binding response regulator (VIMSS) 158, 335
GSU1941 GSU1941 sensor histidine kinase (VIMSS) 159, 335
GSU2285 GSU2285 HD domain protein (NCBI) 173, 318
GSU2455 GSU2455 conserved hypothetical protein (VIMSS) 163, 335
GSU2524 GSU2524 sigma-54 dependent DNA-binding response regulator (VIMSS) 173, 291
GSU2710 GSU2710 hypothetical protein (NCBI) 140, 335
GSU2717 GSU2717 conserved hypothetical protein (VIMSS) 144, 335
GSU3108 rho transcription termination factor Rho (NCBI) 183, 335
GSU3209 GSU3209 iojap-related protein (VIMSS) 160, 335
GSU3282 GSU3282 siroheme synthase, N-terminal domain protein (NCBI) 260, 335
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 GSU0551
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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