Organism : Geobacter sulfurreducens | Module List :
GSU2000 miaA

tRNA delta(2)-isopentenylpyrophosphate transferase (NCBI)

CircVis
Functional Annotations (9)
Function System
tRNA delta(2)-isopentenylpyrophosphate transferase cog/ cog
dimethylallyltranstransferase activity go/ molecular_function
ATP binding go/ molecular_function
tRNA processing go/ biological_process
biosynthetic process go/ biological_process
tRNA dimethylallyltransferase activity go/ molecular_function
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
miaA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2000
(Mouseover regulator name to see its description)

GSU2000 is regulated by 14 influences and regulates 0 modules.
Regulators for GSU2000 miaA (14)
Regulator Module Operator
GSU0063 260 tf
GSU0147 260 tf
GSU0359 260 tf
GSU1495 260 tf
GSU2033 260 tf
GSU2041 260 tf
GSU2571 260 tf
GSU3087 260 tf
GSU3370 260 tf
GSU1250 34 tf
GSU2041 34 tf
GSU2581 34 tf
GSU2915 34 tf
GSU3229 34 tf

Warning: GSU2000 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
2228 5.00e+03 CgcaCCCTGtCGCaC
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2229 3.90e+04 AAAGTTTtTT
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2680 2.00e-02 gTGGCggTgCcGGc
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2681 2.10e+01 AAACttcAtgtAaaatagcGg
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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 GSU2000

GSU2000 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
tRNA delta(2)-isopentenylpyrophosphate transferase cog/ cog
dimethylallyltranstransferase activity go/ molecular_function
ATP binding go/ molecular_function
tRNA processing go/ biological_process
biosynthetic process go/ biological_process
tRNA dimethylallyltransferase activity go/ molecular_function
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
miaA tigr/ tigrfam
Module neighborhood information for GSU2000

GSU2000 has total of 30 gene neighbors in modules 34, 260
Gene neighbors (30)
Gene Common Name Description Module membership
GSU0568 GSU0568 hypothetical protein (VIMSS) 47, 260
GSU0759 GSU0759 hypothetical protein (VIMSS) 260, 278
GSU0933 upp uracil phosphoribosyltransferase (NCBI) 145, 260
GSU0954 GSU0954 conserved hypothetical protein (VIMSS) 260, 338
GSU1054 GSU1054 conserved hypothetical protein (VIMSS) 34, 153
GSU1073 GSU1073 conserved hypothetical protein (VIMSS) 35, 260
GSU1074 GSU1074 conserved hypothetical protein TIGR01033 (VIMSS) 31, 260
GSU1077 ruvB Holliday junction DNA helicase RuvB (NCBI) 208, 260
GSU1078 GSU1078 chromosomal replication initiator protein DnaA, truncation (NCBI) 226, 260
GSU1327 GSU1327 homocysteine S-methyltransferase domain protein (VIMSS) 79, 260
GSU1344 GSU1344 conserved hypothetical protein (VIMSS) 34, 55
GSU1354 GSU1354 plasmid stabilization system family protein (NCBI) 159, 260
GSU1437 GSU1437 peptidase, M48 family (NCBI) 260, 301
GSU1449 GSU1449 hypothetical protein (VIMSS) 87, 260
GSU1674 GSU1674 hypothetical protein (VIMSS) 260, 338
GSU1802 GSU1802 YjeF family protein (VIMSS) 260, 306
GSU1807 GSU1807 conserved hypothetical protein TIGR00159 (VIMSS) 131, 260
GSU2000 miaA tRNA delta(2)-isopentenylpyrophosphate transferase (NCBI) 34, 260
GSU2058 GSU2058 hypothetical protein (VIMSS) 34, 303
GSU2178 GSU2178 hypothetical protein (VIMSS) 34, 36
GSU2225 b2511 GTP-binding protein Era, putative (NCBI) 198, 260
GSU2298 GSU2298 hypothetical protein (VIMSS) 131, 260
GSU2653 GSU2653 MATE efflux family protein (VIMSS) 27, 34
GSU2714 GSU2714 metallo-beta-lactamase family protein (VIMSS) 34, 165
GSU3148 GSU3148 sensor histidine kinase (VIMSS) 84, 260
GSU3183 GSU3183 hypothetical protein (VIMSS) 191, 260
GSU3228 GSU3228 cytochrome c family protein (VIMSS) 34, 224
GSU3282 GSU3282 siroheme synthase, N-terminal domain protein (NCBI) 260, 335
GSU3323 ppk polyphosphate kinase (NCBI) 131, 260
GSU3413 GSU3413 lipoprotein, putative (VIMSS) 34, 165
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 GSU2000
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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