Organism : Geobacter sulfurreducens | Module List :
GSU2060

pmbA protein, putative (VIMSS)

CircVis
Functional Annotations (1)
Function System
Predicted Zn-dependent proteases and their inactivated homologs cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2060
(Mouseover regulator name to see its description)

GSU2060 is regulated by 15 influences and regulates 0 modules.
Regulators for GSU2060 (15)
Regulator Module Operator
GSU0205 4 tf
GSU0551 4 tf
GSU0735 4 tf
GSU0812 4 tf
GSU1072 4 tf
GSU1483 4 tf
GSU1617 4 tf
GSU2587 4 tf
GSU2771 4 tf
GSU2964 4 tf
GSU3217 4 tf
GSU0280 88 tf
GSU0598 88 tf
GSU2506 88 tf
GSU2670 88 tf

Warning: GSU2060 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
2168 2.60e-01 AaCTGTtaTaGtaaAaTtCaA
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2169 1.50e-01 ATacAaTgAgcgcAtTtCA
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2336 2.40e-02 aAAaCAagccgAgagcAtAG
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2337 1.50e-01 tcaATTTTtataAca
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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 GSU2060

GSU2060 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted Zn-dependent proteases and their inactivated homologs cog/ cog
Module neighborhood information for GSU2060

GSU2060 has total of 54 gene neighbors in modules 4, 88
Gene neighbors (54)
Gene Common Name Description Module membership
GSU0015 GSU0015 PPIC-type PPIASE domain protein (NCBI) 4, 89
GSU0016 ppiD PPIC-type PPIASE domain protein (NCBI) 4, 89
GSU0017 mfd transcription-repair coupling factor (NCBI) 4, 262
GSU0018 GSU0018 transcriptional regulator, GntR family/aminotransferase class-I (VIMSS) 4, 89
GSU0019 GSU0019 pentapeptide repeat domain protein (VIMSS) 4, 89
GSU0100 GSU0100 hypothetical protein (VIMSS) 88, 299
GSU0253 GSU0253 sensory box histidine kinase (VIMSS) 4, 107
GSU0256 GSU0256 conserved hypothetical protein (NCBI) 88, 319
GSU0280 GSU0280 transcriptional regulator, Fis family (VIMSS) 76, 88
GSU0452 GSU0452 sensor histidine kinase (VIMSS) 4, 160
GSU0609 purH phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase (NCBI) 88, 231
GSU0816 GSU0816 ABC transporter, ATP-binding protein (VIMSS) 88, 158
GSU1066 GSU1066 hypothetical protein (NCBI) 4, 157
GSU1167 GSU1167 conserved hypothetical protein (VIMSS) 4, 86
GSU1217 GSU1217 hypothetical protein (VIMSS) 88, 146
GSU1234 sppA-2 signal peptide peptidase SppA, 36K type (NCBI) 35, 88
GSU1237 GSU1237 pyridine nucleotide-disulphide oxidoreductase family protein (NCBI) 4, 72
GSU1390 GSU1390 DNA-binding protein (NCBI) 88, 249
GSU1509 GSU1509 glycosyl transferase, group 2 family protein (VIMSS) 88, 124
GSU1638 GSU1638 conserved domain protein (NCBI) 88, 314
GSU1654 GSU1654 response regulator, putative (NCBI) 4, 140
GSU1667 GSU1667 hypothetical protein (VIMSS) 88, 124
GSU1683 GSU1683 conserved hypothetical protein (VIMSS) 4, 235
GSU1705 panB 3-methyl-2-oxobutanoate hydroxymethyltransferase (NCBI) 88, 290
GSU1835 glnA glutamine synthetase, type I (NCBI) 4, 72
GSU1836 GSU1836 nitrogen regulatory protein P-II (VIMSS) 4, 72
GSU1910 ilvN acetolactate synthase, small subunit (NCBI) 88, 276
GSU1962 GSU1962 glycosyl transferase, group 2 family protein (VIMSS) 88, 191
GSU2060 GSU2060 pmbA protein, putative (VIMSS) 4, 88
GSU2061 argA acetyltransferase, GNAT family (NCBI) 4, 88
GSU2062 GSU2062 GGDEF domain protein (VIMSS) 4, 88
GSU2063 GSU2063 HD domain protein (NCBI) 4, 88
GSU2066 glgP glycogen phosphorylase (NCBI) 88, 201
GSU2067 GSU2067 ATPase, AAA family (VIMSS) 88, 327
GSU2068 GSU2068 6-phosphofructokinase (VIMSS) 88, 121
GSU2192 cbbZ phosphoglycolate phosphatase (NCBI) 4, 40
GSU2193 GSU2193 conserved hypothetical protein (VIMSS) 4, 193
GSU2371 trpA tryptophan synthase, alpha subunit (NCBI) 88, 148
GSU2376 GSU2376 hypothetical protein (VIMSS) 88, 327
GSU2439 relE RelE protein (NCBI) 88, 269
GSU2474 GSU2474 hypothetical protein (VIMSS) 88, 181
GSU2627 bioC biotin biosynthesis protein (Dmitry Rodionov) 88, 149
GSU2628 bioH biotin biosynthesis protein (Dmitry Rodionov) 88, 149
GSU2629 bioF 8-amino-7-oxononanoate synthase (NCBI) 88, 149
GSU2631 GSU2631 conserved hypothetical protein TIGR00149 (VIMSS) 76, 88
GSU2712 GSU2712 hypothetical protein (VIMSS) 4, 12
GSU2713 GSU2713 conserved hypothetical protein (VIMSS) 4, 133
GSU2762 glpK glycerol kinase (NCBI) 4, 252
GSU2763 GSU2763 conserved hypothetical protein (VIMSS) 4, 66
GSU3114 GSU3114 hypothetical protein (VIMSS) 4, 100
GSU3140 GSU3140 peptidase, M1 family protein (NCBI) 4, 100
GSU3141 GSU3141 hypothetical protein (VIMSS) 4, 216
GSU3142 GSU3142 phospho-2-dehydro-3-deoxyheptonate aldolase (NCBI) 4, 216
GSU3208 GSU3208 conserved hypothetical protein (NCBI) 88, 121
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 GSU2060
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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