Organism : Geobacter sulfurreducens | Module List :
GSU0443

ribonuclease D, putative (VIMSS)

CircVis
Functional Annotations (7)
Function System
Ribonuclease D cog/ cog
nucleotide binding go/ molecular_function
nucleic acid binding go/ molecular_function
ribonuclease III activity go/ molecular_function
intracellular go/ cellular_component
nucleobase-containing compound metabolic process go/ biological_process
3'-5' exonuclease activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0443
(Mouseover regulator name to see its description)

GSU0443 is regulated by 15 influences and regulates 0 modules.
Regulators for GSU0443 (15)
Regulator Module Operator
GSU0164 295 tf
GSU1320 295 tf
GSU1483 295 tf
GSU1653 295 tf
GSU2753 295 tf
GSU2964 295 tf
GSU3396 295 tf
GSU0655 89 tf
GSU1003 89 tf
GSU1617 89 tf
GSU2177 89 tf
GSU2698 89 tf
GSU3087 89 tf
GSU3298 89 tf
GSU3396 89 tf

Warning: GSU0443 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
2338 2.30e-02 C.aTGAAA.aaattACAaCAg
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2339 1.10e-01 aAAAcGCaAtCtTTgttTt
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2748 1.20e+03 AaATctatTGATtcT
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2749 7.30e+03 TTTACATGaAaT.T
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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 GSU0443

GSU0443 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Ribonuclease D cog/ cog
nucleotide binding go/ molecular_function
nucleic acid binding go/ molecular_function
ribonuclease III activity go/ molecular_function
intracellular go/ cellular_component
nucleobase-containing compound metabolic process go/ biological_process
3'-5' exonuclease activity go/ molecular_function
Module neighborhood information for GSU0443

GSU0443 has total of 55 gene neighbors in modules 89, 295
Gene neighbors (55)
Gene Common Name Description Module membership
GSU0010 GSU0010 sensory box histidine kinase/response regulator (VIMSS) 39, 295
GSU0015 GSU0015 PPIC-type PPIASE domain protein (NCBI) 4, 89
GSU0016 ppiD PPIC-type PPIASE domain protein (NCBI) 4, 89
GSU0018 GSU0018 transcriptional regulator, GntR family/aminotransferase class-I (VIMSS) 4, 89
GSU0019 GSU0019 pentapeptide repeat domain protein (VIMSS) 4, 89
GSU0249 GSU0249 membrane protein, putative (VIMSS) 55, 295
GSU0386 radC DNA repair protein RadC (NCBI) 89, 283
GSU0387 GSU0387 undecaprenol kinase, putative (VIMSS) 89, 295
GSU0388 GSU0388 conserved hypothetical protein (NCBI) 89, 264
GSU0389 GSU0389 phosphate transporter, putative (VIMSS) 26, 89
GSU0443 GSU0443 ribonuclease D, putative (VIMSS) 89, 295
GSU0529 nfo endonuclease IV (NCBI) 89, 225
GSU0573 GSU0573 alcohol dehydrogenase, zinc-containing (VIMSS) 295, 322
GSU0876 GSU0876 diacylglycerol kinase catalytic domain protein (NCBI) 89, 322
GSU1002 GSU1002 isochorismatase family protein (NCBI) 89, 265
GSU1003 ntrC nitrogen regulation protein NR(I) (NCBI) 89, 265
GSU1004 GSU1004 sensory box histidine kinase (VIMSS) 89, 265
GSU1075 ruvC crossover junction endodeoxyribonuclease RuvC (NCBI) 233, 295
GSU1124 coaBC phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase (NCBI) 126, 295
GSU1172 mviN virulence factor mviN protein (NCBI) 295, 300
GSU1271 pyrB aspartate carbamoyltransferase (NCBI) 39, 295
GSU1292 GSU1292 sensory box histidine kinase (VIMSS) 35, 295
GSU1444 GSU1444 conserved hypothetical protein (VIMSS) 103, 295
GSU1460 proS prolyl-tRNA synthetase (NCBI) 233, 295
GSU1482 GSU1482 outer membrane efflux protein (VIMSS) 14, 295
GSU1653 GSU1653 sigma-54 dependent DNA-binding response regulator (VIMSS) 146, 295
GSU1702 GSU1702 ROK family protein (VIMSS) 204, 295
GSU2053 GSU2053 indolepyruvate ferredoxin oxidoreductase, alpha subunit, putative (VIMSS) 52, 295
GSU2092 GSU2092 conserved hypothetical protein (VIMSS) 142, 295
GSU2214 cheB-3 protein-glutamate methylesterase (NCBI) 126, 295
GSU2215 cheR-3 chemotaxis protein methyltransferase CheR (NCBI) 295, 323
GSU2231 GSU2231 conserved hypothetical protein (VIMSS) 262, 295
GSU2243 GSU2243 UDP-N-acetylglucosamine 2-epimerase (VIMSS) 295, 308
GSU2551 GSU2551 LysM domain protein (VIMSS) 89, 231
GSU2595 GSU2595 hypothetical protein (VIMSS) 27, 295
GSU2596 GSU2596 lipoprotein, putative (VIMSS) 179, 295
GSU2609 pilB type IV pilus assembly protein, putative (NCBI) 227, 295
GSU2619 tgt-2 queuine tRNA-ribosyltransferase (NCBI) 89, 231
GSU2989 GSU2989 L-threonine-O-3-phosphate decarboxylase, putative (VIMSS) 89, 281
GSU2991 GSU2991 sensor histidine kinase (VIMSS) 89, 285
GSU2992 cobQ cobyric acid synthase (NCBI) 89, 153
GSU2997 cbiD cobalamin biosynthesis protein CbiD (NCBI) 89, 281
GSU2998 GSU2998 nitroimidazole resistance protein, putative (VIMSS) 89, 169
GSU3002 GSU3002 cobalt ABC transporter, permease protein (VIMSS) 89, 285
GSU3004 GSU3004 cobalt transport protein CbiM (RefSeq) 75, 89
GSU3008 cobS cobalamin 5'-phosphate synthase (NCBI) 30, 295
GSU3010 cobU bifunctional cobalamin biosynthesis protein CobU (NCBI) 30, 89
GSU3264 GSU3264 membrane protein, putative (VIMSS) 295, 300
GSU3265 nirB sulfite reductase, assimilatory-type (NCBI) 295, 327
GSU3283 GSU3283 cytochrome c biogenesis protein, CcmF/CcyK/CcsA family (VIMSS) 44, 89
GSU3286 hemD uroporphyrinogen III synthase/methyltransferase (NCBI) 89, 300
GSU3287 GSU3287 hydrolase, TatD family (NCBI) 30, 89
GSU3288 moeB thiF family protein (NCBI) 30, 89
GSU3346 GSU3346 potassium uptake protein, Kup system (VIMSS) 249, 295
GSU3396 GSU3396 transcriptional regulator, GntR family (VIMSS) 178, 295
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 GSU0443
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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