Organism : Geobacter sulfurreducens | Module List :
GSU1485 vacB

ribonuclease R, putative (NCBI)

CircVis
Functional Annotations (7)
Function System
Exoribonuclease R cog/ cog
RNA binding go/ molecular_function
ribonuclease activity go/ molecular_function
exoribonuclease II activity go/ molecular_function
RNA metabolic process go/ biological_process
RNA degradation kegg/ kegg pathway
3_prime_RNase tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1485
(Mouseover regulator name to see its description)

GSU1485 is regulated by 16 influences and regulates 0 modules.
Regulators for GSU1485 vacB (16)
Regulator Module Operator
GSU0041 222 tf
GSU0164 222 tf
GSU0896 222 tf
GSU1495 222 tf
GSU1569 222 tf
GSU1992 222 tf
GSU2987 222 tf
GSU3370 222 tf
GSU0031 329 tf
GSU0041 329 tf
GSU0187 329 tf
GSU0280 329 tf
GSU1218 329 tf
GSU1495 329 tf
GSU2753 329 tf
GSU3045 329 tf

Warning: GSU1485 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
2604 4.70e-01 cttaaaTtcT..CcGcAAgGggAC
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2605 3.30e+02 AAaaTGcaAagGgTTTTTcaGTGa
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2814 7.70e+04 TTTTTcAGT
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2815 3.10e+01 tTTtcaCgGaaAAg
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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 GSU1485

GSU1485 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Exoribonuclease R cog/ cog
RNA binding go/ molecular_function
ribonuclease activity go/ molecular_function
exoribonuclease II activity go/ molecular_function
RNA metabolic process go/ biological_process
RNA degradation kegg/ kegg pathway
3_prime_RNase tigr/ tigrfam
Module neighborhood information for GSU1485

GSU1485 has total of 34 gene neighbors in modules 222, 329
Gene neighbors (34)
Gene Common Name Description Module membership
GSU0156 argH argininosuccinate lyase (NCBI) 222, 289
GSU0157 GSU0157 fibronectin type III domain protein (NCBI) 71, 222
GSU0257 GSU0257 conserved hypothetical protein (VIMSS) 198, 222
GSU0258 GSU0258 hypothetical protein (VIMSS) 59, 222
GSU0259 GSU0259 flavoredoxin (VIMSS) 47, 222
GSU0461 fabG-1 3-oxoacyl-(acyl carrier protein) reductase (NCBI) 67, 222
GSU0565 GSU0565 hypothetical protein (VIMSS) 163, 222
GSU0567 tag DNA-3-methyladenine glycosylase I (NCBI) 232, 329
GSU0631 GSU0631 glycosyl transferase, group 2 family protein (VIMSS) 68, 329
GSU0632 GSU0632 conserved hypothetical protein (VIMSS) 201, 329
GSU0637 GSU0637 conserved hypothetical protein (VIMSS) 68, 329
GSU0742 GSU0742 NAD-dependent dehydrogenase subunit (VIMSS) 222, 265
GSU0796 GSU0796 acyl-CoA thioester hydrolase, putative (NCBI) 213, 222
GSU0867 ubiE ubiquinone/menaquinone biosynthesis methyltransferase UbiE, putative (NCBI) 30, 329
GSU1137 GSU1137 KH domain/HD domain protein (NCBI) 207, 222
GSU1173 ogt methylated-DNA--protein-cysteine methyltransferase, putative (NCBI) 219, 222
GSU1179 GSU1179 hypothetical protein (NCBI) 29, 329
GSU1275 GSU1275 conserved hypothetical protein (VIMSS) 148, 329
GSU1462 GSU1462 RNA methyltransferase, TrmH family, group 3 (VIMSS) 204, 329
GSU1484 GSU1484 soluble lytic murein transglycosylase, putative (VIMSS) 204, 222
GSU1485 vacB ribonuclease R, putative (NCBI) 222, 329
GSU1488 GSU1488 membrane protein, putative (VIMSS) 75, 222
GSU1700 maeB NADP-dependent malic enzyme (NCBI) 204, 329
GSU1701 GSU1701 HIT family protein (VIMSS) 204, 329
GSU1704 GSU1704 methyl-accepting chemotaxis protein, putative (VIMSS) 156, 329
GSU1768 GSU1768 ParA family protein (VIMSS) 176, 329
GSU1778 GSU1778 type II secretion system protein, putative (VIMSS) 316, 329
GSU1897 GSU1897 MTA/SAH nucleosidase, putative (VIMSS) 232, 329
GSU1991 GSU1991 CAAX amino terminal protease family protein (NCBI) 222, 278
GSU2125 GSU2125 conserved domain protein (VIMSS) 59, 222
GSU2222 cheA-2 chemotaxis protein CheA (NCBI) 126, 222
GSU2947 GSU2947 sensor histidine kinase (VIMSS) 67, 222
GSU3110 GSU3110 hypothetical protein (VIMSS) 262, 329
GSU3164 GSU3164 hypothetical protein (VIMSS) 222, 334
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 GSU1485
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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