Organism : Geobacter sulfurreducens | Module List :
GSU3309

conserved hypothetical protein (VIMSS)

CircVis
Functional Annotations (2)
Function System
ATP binding go/ molecular_function
ATPase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3309
(Mouseover regulator name to see its description)

GSU3309 is regulated by 15 influences and regulates 0 modules.
Regulators for GSU3309 (15)
Regulator Module Operator
GSU0178 121 tf
GSU0266 121 tf
GSU1410 121 tf
GSU1831 121 tf
GSU1989 121 tf
GSU2524 121 tf
GSU3370 121 tf
GSU0280 51 tf
GSU0770 51 tf
GSU1293 51 tf
GSU1495 51 tf
GSU1831 51 tf
GSU2524 51 tf
GSU3387 51 tf
GSU3396 51 tf

Warning: GSU3309 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
2262 5.00e+03 TtTCctttgg.
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2263 3.10e+04 TcagTttaTTcaCgtaATact
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2402 6.70e+00 atGaacttaActttcagTT
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2403 8.40e+02 TaTCcCTtgtgttagaacaaaAAa
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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 GSU3309

GSU3309 is enriched for 2 functions in 2 categories.
Enrichment Table (2)
Function System
ATP binding go/ molecular_function
ATPase activity go/ molecular_function
Module neighborhood information for GSU3309

GSU3309 has total of 44 gene neighbors in modules 51, 121
Gene neighbors (44)
Gene Common Name Description Module membership
GSU0462 GSU0462 peptidase, M48 family (NCBI) 51, 63
GSU0463 GSU0463 membrane protein, putative (VIMSS) 36, 51
GSU0501 GSU0501 lipoprotein, putative (VIMSS) 114, 121
GSU0503 crcB crcB protein (NCBI) 77, 121
GSU0504 GSU0504 conserved hypothetical protein (VIMSS) 121, 284
GSU0508 GSU0508 conserved hypothetical protein TIGR00247 (NCBI) 7, 121
GSU0617 GSU0617 NHL repeat domain protein (VIMSS) 121, 148
GSU0702 GSU0702 cytochrome c family protein (VIMSS) 51, 76
GSU0729 GSU0729 iron-sulfur cluster-binding protein (VIMSS) 121, 291
GSU0877 GSU0877 response regulator (VIMSS) 51, 76
GSU0927 GSU0927 peptidase, M16 family (NCBI) 20, 121
GSU1151 GSU1151 conserved hypothetical protein (VIMSS) 121, 277
GSU1155 GSU1155 glutaredoxin family protein (VIMSS) 51, 293
GSU1202 rfbA mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase, truncation (NCBI) 51, 144
GSU1379 fur ferric uptake regulation protein (Dmitry Rodionov) 81, 121
GSU1381 GSU1381 hypothetical protein (VIMSS) 121, 324
GSU1490 aroE shikimate 5-dehydrogenase (NCBI) 83, 121
GSU1491 GSU1491 type IV pilus biogenesis protein PilB (VIMSS) 51, 75
GSU1564 GSU1564 Glu/Leu/Phe/Val dehydrogenase family protein (NCBI) 51, 76
GSU1571 GSU1571 conserved domain protein (NCBI) 121, 153
GSU1572 GSU1572 ribD domain protein (NCBI) 51, 79
GSU1643 pleD GGDEF/response regulator receiver domain protein (NCBI) 51, 293
GSU1679 GSU1679 hypothetical protein (VIMSS) 51, 249
GSU1715 GSU1715 hypothetical protein (VIMSS) 51, 181
GSU2068 GSU2068 6-phosphofructokinase (VIMSS) 88, 121
GSU2129 GSU2129 hypothetical protein (VIMSS) 121, 324
GSU2131 GSU2131 hypothetical protein (VIMSS) 51, 66
GSU2144 GSU2144 sensor histidine kinase (VIMSS) 121, 294
GSU2194 guaA GMP synthase (NCBI) 51, 201
GSU2216 GSU2216 PBS lyase HEAT-like repeat protein (NCBI) 51, 293
GSU2224 GSU2224 response regulator (VIMSS) 51, 201
GSU2377 GSU2377 hypothetical protein (VIMSS) 51, 158
GSU2393 GSU2393 ISGsu5, transposase, truncation (VIMSS) 121, 189
GSU2450 GSU2450 conserved hypothetical protein (VIMSS) 51, 59
GSU2453 GSU2453 membrane protein, putative (VIMSS) 51, 79
GSU2554 GSU2554 conserved hypothetical protein (VIMSS) 51, 231
GSU2773 GSU2773 conserved domain protein (VIMSS) 51, 179
GSU2789 GSU2789 sensory box histidine kinase (VIMSS) 121, 269
GSU2995 cobI precorrin-2 C20-methyltransferase (NCBI) 51, 76
GSU3171 GSU3171 conserved domain protein (NCBI) 51, 103
GSU3208 GSU3208 conserved hypothetical protein (NCBI) 88, 121
GSU3212 proB glutamate 5-kinase (NCBI) 121, 160
GSU3250 pcnB polyA polymerase (NCBI) 51, 73
GSU3309 GSU3309 conserved hypothetical protein (VIMSS) 51, 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 GSU3309
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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