Organism : Geobacter sulfurreducens | Module List :
GSU1228

cytochrome c family protein (VIMSS)

CircVis
Functional Annotations (1)
Function System
paired_CXXCH_1 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1228
(Mouseover regulator name to see its description)

GSU1228 is regulated by 23 influences and regulates 0 modules.
Regulators for GSU1228 (23)
Regulator Module Operator
GSU0254 11 tf
GSU0266 11 tf
GSU0372 11 tf
GSU1115 11 tf
GSU1727 11 tf
GSU2587 11 tf
GSU2915 11 tf
GSU3387 11 tf
GSU3421 11 tf
GSU0013 147 tf
GSU0107 147 tf
GSU0254 147 tf
GSU0655 147 tf
GSU1013 147 tf
GSU1268 147 tf
GSU1345 147 tf
GSU1626 147 tf
GSU1887 147 tf
GSU2362 147 tf
GSU2523 147 tf
GSU3108 147 tf
GSU3363 147 tf
GSU3387 147 tf

Warning: GSU1228 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
2182 4.20e-02 gAaGgcCgctacCcg.CcGacgtt
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2183 2.20e+02 AAcaAtcAAAt
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2454 1.10e+03 AtAAaaaCCTT.ACAAACggT
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2455 2.00e+04 acCacgAgcccGGaGGaAataCcg
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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 GSU1228

GSU1228 is enriched for 1 functions in 4 categories.
Enrichment Table (1)
Function System
paired_CXXCH_1 tigr/ tigrfam
Module neighborhood information for GSU1228

GSU1228 has total of 49 gene neighbors in modules 11, 147
Gene neighbors (49)
Gene Common Name Description Module membership
GSU0007 GSU0007 sensory box histidine kinase (VIMSS) 147, 159
GSU0107 spo0J parB-like domain protein (NCBI) 147, 181
GSU0301 GSU0301 lytic murein transglycosylase, putative (VIMSS) 11, 197
GSU0390 GSU0390 conserved hypothetical protein (VIMSS) 11, 18
GSU0446 GSU0446 conserved hypothetical protein TIGR00046 (VIMSS) 147, 183
GSU0606 alr alanine racemase (NCBI) 147, 231
GSU0607 selD selenide, water dikinase, selenocysteine-containing (NCBI) 147, 231
GSU0652 nadE NAD+ synthetase (NCBI) 11, 197
GSU0654 moeB thiF family protein (NCBI) 11, 315
GSU0679 GSU0679 tellurite resistance protein-related protein (VIMSS) 25, 147
GSU0689 GSU0689 protein export membrane protein, SecD/SecF family, putative (VIMSS) 147, 309
GSU0751 GSU0751 conserved hypothetical protein (VIMSS) 147, 183
GSU0906 rpsU-1 ribosomal protein S21 (NCBI) 11, 248
GSU0932 uraA uracil permease (NCBI) 147, 164
GSU0992 GSU0992 hypothetical protein (VIMSS) 11, 250
GSU1227 GSU1227 ABC transporter, ATP-binding protein (VIMSS) 11, 147
GSU1228 GSU1228 cytochrome c family protein (VIMSS) 11, 147
GSU1233 GSU1233 phosphoesterase, putative (NCBI) 11, 50
GSU1291 GSU1291 response regulator (VIMSS) 147, 158
GSU1377 GSU1377 3-hydroxybutyryl-CoA dehydratase (VIMSS) 11, 126
GSU1527 GSU1527 conserved hypothetical protein (VIMSS) 147, 183
GSU1541 GSU1541 conserved hypothetical protein (VIMSS) 13, 147
GSU1543 GSU1543 hypothetical protein (VIMSS) 147, 262
GSU1706 panC pantoate--beta-alanine ligase (NCBI) 11, 125
GSU1746 ihfB integration host factor, beta subunit (NCBI) 11, 265
GSU1749 GSU1749 hypothetical protein (VIMSS) 11, 70
GSU1838 hrpB ATP-dependent helicase HrpB (NCBI) 147, 338
GSU1917 uppS undecaprenyl diphosphate synthase (NCBI) 147, 333
GSU2021 pepQ-2 xaa-pro dipeptidase (NCBI) 11, 309
GSU2023 GSU2023 conserved hypothetical protein (VIMSS) 11, 262
GSU2078 rodA rod shape-determining protein RodA (NCBI) 147, 207
GSU2287 GSU2287 response regulator (VIMSS) 11, 46
GSU2334 GSU2334 hypothetical protein (VIMSS) 59, 147
GSU2545 maf maf protein (NCBI) 42, 147
GSU2647 GSU2647 conserved hypothetical protein (VIMSS) 11, 147
GSU2694 GSU2694 hypothetical protein (VIMSS) 17, 147
GSU2727 GSU2727 hypothetical protein (VIMSS) 11, 147
GSU2756 GSU2756 hypothetical protein (VIMSS) 147, 176
GSU2783 GSU2783 HDIG domain protein (VIMSS) 147, 296
GSU2915 GSU2915 sigma-54 dependent DNA-binding response regulator (VIMSS) 11, 116
GSU3205 GSU3205 MiaB-like tRNA modifying enzyme YliG (NCBI) 47, 147
GSU3294 GSU3294 rubredoxin-oxygen oxidoreductase, putative (VIMSS) 11, 258
GSU3307 hisS histidyl-tRNA synthetase, putative (NCBI) 147, 245
GSU3318 GSU3318 conserved hypothetical protein (VIMSS) 11, 50
GSU3320 prmA ribosomal protein L11 methyltransferase, putative (NCBI) 11, 50
GSU3321 GSU3321 phosphoglucomutase/phosphomannomutase family protein (VIMSS) 11, 50
GSU3322 corA-2 magnesium and cobalt transport protein CorA (NCBI) 11, 50
GSU3353 rluD RNA pseudouridine synthase family protein (NCBI) 147, 289
GSU3405 GSU3405 amino acid ABC transporter, permease protein (VIMSS) 11, 18
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 GSU1228
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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