Organism : Geobacter sulfurreducens | Module List :
GSU1126

phage SPO1 DNA polymerase-related protein (VIMSS)

CircVis
Functional Annotations (3)
Function System
Uracil-DNA glycosylase cog/ cog
DNA-directed DNA polymerase activity go/ molecular_function
UDG_fam4 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1126
(Mouseover regulator name to see its description)

GSU1126 is regulated by 13 influences and regulates 0 modules.
Regulators for GSU1126 (13)
Regulator Module Operator
GSU0372 101 tf
GSU1270 101 tf
GSU1483 101 tf
GSU2237 101 tf
GSU2524 101 tf
GSU3087 101 tf
GSU0735 225 tf
GSU0770 225 tf
GSU1115 225 tf
GSU1989 225 tf
GSU2041 225 tf
GSU2941 225 tf
GSU3087 225 tf

Warning: GSU1126 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
2362 4.20e-02 TaaAcAAA
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2363 3.40e+00 aAAgTGTaTaCagtAtgC
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2610 6.20e+02 GGggccggcGgtgctgcgg.ag
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2611 3.20e+04 GAggaaggagAAcgg
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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 GSU1126

GSU1126 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Uracil-DNA glycosylase cog/ cog
DNA-directed DNA polymerase activity go/ molecular_function
UDG_fam4 tigr/ tigrfam
Module neighborhood information for GSU1126

GSU1126 has total of 44 gene neighbors in modules 101, 225
Gene neighbors (44)
Gene Common Name Description Module membership
GSU0159 dapA dihydrodipicolinate synthase (NCBI) 101, 214
GSU0490 GSU0490 acetyl-CoA hydrolase/transferase family protein (VIMSS) 140, 225
GSU0509 sfrA Fe(III) reductase, alpha subunit (NCBI) 101, 243
GSU0510 sfrB Fe(III) reductase, beta subunit (NCBI) 101, 243
GSU0519 GSU0519 conserved hypothetical protein (VIMSS) 99, 225
GSU0529 nfo endonuclease IV (NCBI) 89, 225
GSU0577 recO DNA repair protein RecO (NCBI) 160, 225
GSU0669 GSU0669 hypothetical protein (VIMSS) 173, 225
GSU0823 ppiC peptidyl-prolyl cis-trans isomerase C (NCBI) 197, 225
GSU0824 GSU0824 conserved hypothetical protein (VIMSS) 197, 225
GSU0864 GSU0864 conserved hypothetical protein TIGR00251 (VIMSS) 101, 214
GSU0905 GSU0905 hypothetical protein (NCBI) 128, 225
GSU0994 fumB fumarate hydratase, class I (NCBI) 101, 243
GSU1045 GSU1045 membrane protein, putative (NCBI) 128, 225
GSU1106 GSU1106 citrate synthase (NCBI) 101, 243
GSU1126 GSU1126 phage SPO1 DNA polymerase-related protein (VIMSS) 101, 225
GSU1176 GSU1176 fumarate reductase, cytochrome b subunit, putative (VIMSS) 101, 228
GSU1177 frdA fumarate reductase, flavoprotein subunit (NCBI) 101, 214
GSU1178 frdB fumarate reductase, iron-sulfur protein (NCBI) 225, 228
GSU1375 GSU1375 hypothetical protein (VIMSS) 169, 225
GSU1465 icd isocitrate dehydrogenase, NADP-dependent (NCBI) 101, 297
GSU1466 mdh malate dehydrogenase (NCBI) 101, 297
GSU1515 thrS threonyl-tRNA synthetase (NCBI) 101, 116
GSU1657 GSU1657 DNA internalization-related competence protein ComEC/Rec2 (VIMSS) 8, 225
GSU1660 acnB aconitate hydratase 2 (NCBI) 101, 169
GSU1902 leuD 3-isopropylmalate dehydratase, small subunit, putative (NCBI) 101, 169
GSU2219 pleD response regulator (NCBI) 225, 309
GSU2223 cheY-6 chemotaxis protein CheY (NCBI) 101, 238
GSU2340 GSU2340 Na+/H+ ion antiporter family protein (NCBI) 153, 225
GSU2426 GSU2426 conserved hypothetical protein (NCBI) 208, 225
GSU2427 GSU2427 hypothetical protein (VIMSS) 101, 225
GSU2680 GSU2680 conserved hypothetical protein (VIMSS) 140, 225
GSU2707 ackA-1 acetate kinase (NCBI) 101, 168
GSU2708 GSU2708 ferredoxin family protein (VIMSS) 101, 228
GSU2765 GSU2765 hypothetical protein (VIMSS) 208, 225
GSU2958 GSU2958 thiol:disulfide interchange protein, putative (NCBI) 146, 225
GSU3005 thiC-2 thiamine biosynthesis protein ThiC (NCBI) 101, 169
GSU3007 GSU3007 phosphoglycerate mutase family, putative (VIMSS) 101, 169
GSU3009 cobT nicotinate-nucleotide--dimethylbenzimidazolephosphoribosyltransferase (NCBI) 101, 169
GSU3011 GSU3011 hypothetical protein (VIMSS) 97, 101
GSU3129 GSU3129 MATE efflux family protein (NCBI) 78, 225
GSU3134 GSU3134 hypothetical protein (VIMSS) 80, 225
GSU3302 mutB methylmalonyl-CoA mutase, putative (NCBI) 215, 225
GSU3349 GSU3349 cyclase, putative (NCBI) 128, 225
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 GSU1126
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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