Organism : Geobacter sulfurreducens | Module List :
GSU2071 rnhA

ribonuclease HI (NCBI)

CircVis
Functional Annotations (4)
Function System
Ribonuclease HI cog/ cog
nucleic acid binding go/ molecular_function
ribonuclease H activity go/ molecular_function
DNA replication kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2071
(Mouseover regulator name to see its description)

GSU2071 is regulated by 18 influences and regulates 0 modules.
Regulators for GSU2071 rnhA (18)
Regulator Module Operator
GSU0205 327 tf
GSU0366 327 tf
GSU1268 327 tf
GSU1483 327 tf
GSU1653 327 tf
GSU2041 327 tf
GSU2524 327 tf
GSU2716 327 tf
GSU2779 327 tf
GSU0031 7 tf
GSU0280 7 tf
GSU0366 7 tf
GSU0581 7 tf
GSU1495 7 tf
GSU1522 7 tf
GSU2625 7 tf
GSU2753 7 tf
GSU3298 7 tf

Warning: GSU2071 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
2174 6.00e+03 GAAataAa
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2175 3.40e+04 ATAAta.a.aagCAtCcgtg.gGa
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2810 2.20e+03 tttttcttTgATaGtaa.gTtCa
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2811 1.10e+03 AAAAaGAt
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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 GSU2071

GSU2071 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Ribonuclease HI cog/ cog
nucleic acid binding go/ molecular_function
ribonuclease H activity go/ molecular_function
DNA replication kegg/ kegg pathway
Module neighborhood information for GSU2071

GSU2071 has total of 38 gene neighbors in modules 7, 327
Gene neighbors (38)
Gene Common Name Description Module membership
GSU0117 GSU0117 aminotransferase, classes I and II (NCBI) 7, 248
GSU0508 GSU0508 conserved hypothetical protein TIGR00247 (NCBI) 7, 121
GSU0557 GSU0557 conserved hypothetical protein, interruption-C (NCBI) 7, 68
GSU0817 GSU0817 conserved hypothetical protein (VIMSS) 7, 210
GSU1108 GSU1108 aldehyde dehydrogenase family protein (NCBI) 230, 327
GSU1266 lepA GTP-binding protein LepA (NCBI) 7, 176
GSU1512 GSU1512 amine oxidase, flavin-containing (NCBI) 313, 327
GSU1630 GSU1630 sensory box histidine kinase (VIMSS) 238, 327
GSU1773 GSU1773 M23/M37 peptidase domain protein (VIMSS) 7, 83
GSU1879 GSU1879 DNA-binding response regulator (VIMSS) 7, 76
GSU1960 GSU1960 hexapeptide transferase family protein (VIMSS) 191, 327
GSU1963 GSU1963 polysaccharide biosynthesis domain protein (VIMSS) 191, 327
GSU2030 GSU2030 type IV pilus biogenesis protein PilO (VIMSS) 7, 76
GSU2031 GSU2031 type IV pilus biogenesis protein PilN (VIMSS) 7, 76
GSU2043 pilD type 4 prepilin-like proteins leader peptide processing enzyme (NCBI) 15, 327
GSU2067 GSU2067 ATPase, AAA family (VIMSS) 88, 327
GSU2069 GSU2069 HAD-superfamily hydrolase, subfamily IA, variant 1 (NCBI) 7, 68
GSU2070 GSU2070 HNH endonuclease family protein (NCBI) 7, 68
GSU2071 rnhA ribonuclease HI (NCBI) 7, 327
GSU2072 GSU2072 1-acyl-sn-glycerol-3-phosphate acyltransferase, putative (VIMSS) 7, 248
GSU2079 mrdA penicillin-binding protein 2 (NCBI) 7, 67
GSU2081 mreC rod shape-determining protein MreC (NCBI) 7, 137
GSU2121 GSU2121 Transglycosylase SLT domain protein (VIMSS) 60, 327
GSU2204 GSU2204 cytochrome c family protein, putative (NCBI) 300, 327
GSU2356 GSU2356 hypothetical protein (VIMSS) 7, 311
GSU2376 GSU2376 hypothetical protein (VIMSS) 88, 327
GSU2547 gid gid protein (NCBI) 7, 30
GSU2548 GSU2548 hypothetical protein (VIMSS) 7, 29
GSU2686 GSU2686 ABC transporter, ATP-binding protein (VIMSS) 49, 327
GSU2736 GSU2736 hypothetical protein (VIMSS) 164, 327
GSU2758 uvrA excinuclease ABC family protein (NCBI) 240, 327
GSU2927 GSU2927 cytochrome c, putative (NCBI) 181, 327
GSU3173 GSU3173 conserved hypothetical protein (VIMSS) 103, 327
GSU3265 nirB sulfite reductase, assimilatory-type (NCBI) 295, 327
GSU3276 GSU3276 LysM domain protein (NCBI) 281, 327
GSU3298 GSU3298 transcriptional regulator, Cro/CI family (VIMSS) 7, 248
GSU3300 GSU3300 biotin-requiring enzyme subunit (NCBI) 230, 327
GSU3386 GSU3386 lipoprotein, putative (VIMSS) 327, 336
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 GSU2071
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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