Organism : Geobacter sulfurreducens | Module List :
GSU2386

methylcobamide:CoM methyltransferase-related protein (NCBI)

CircVis
Functional Annotations (3)
Function System
Uroporphyrinogen-III decarboxylase cog/ cog
uroporphyrinogen decarboxylase activity go/ molecular_function
porphyrin-containing compound biosynthetic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2386
(Mouseover regulator name to see its description)

GSU2386 is regulated by 20 influences and regulates 0 modules.
Regulators for GSU2386 (20)
Regulator Module Operator
GSU0254 189 tf
GSU0266 189 tf
GSU0372 189 tf
GSU1115 189 tf
GSU1268 189 tf
GSU1940 189 tf
GSU2033 189 tf
GSU2915 189 tf
GSU3087 189 tf
GSU0254 266 tf
GSU0473 266 tf
GSU1095 266 tf
GSU1115 266 tf
GSU1410 266 tf
GSU1522 266 tf
GSU2041 266 tf
GSU2523 266 tf
GSU2587 266 tf
GSU2915 266 tf
GSU3387 266 tf

Warning: GSU2386 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
2538 7.60e+04 ttcCgt.CCT.tT.tT.aTcgag
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2539 5.10e+04 AtccGtTcatccTgA
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2692 6.20e+01 CGgccGgC.GG
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2693 3.80e+04 TATTtCAAcTCAATAtAT
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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 GSU2386

GSU2386 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Uroporphyrinogen-III decarboxylase cog/ cog
uroporphyrinogen decarboxylase activity go/ molecular_function
porphyrin-containing compound biosynthetic process go/ biological_process
Module neighborhood information for GSU2386

GSU2386 has total of 54 gene neighbors in modules 189, 266
Gene neighbors (54)
Gene Common Name Description Module membership
GSU0027 GSU0027 TolR protein (VIMSS) 57, 266
GSU0028 tolQ tolQ protein (NCBI) 184, 266
GSU0030 GSU0030 oxygen-independent coproporphyrinogen III oxidase, putative (VIMSS) 118, 266
GSU0032 grpE GrpE protein (NCBI) 184, 266
GSU0062 GSU0062 TraD protein, putative (VIMSS) 189, 319
GSU0121 GSU0121 nickel-iron hydrogenase, b-type cytochrome subunit (VIMSS) 14, 266
GSU0150 argB acetylglutamate kinase (NCBI) 107, 189
GSU0206 GSU0206 ZIP zinc transporter family protein (VIMSS) 189, 206
GSU0218 GSU0218 conserved hypothetical protein (VIMSS) 21, 266
GSU0231 GSU0231 hypothetical protein (VIMSS) 189, 224
GSU0296 cheA chemotaxis protein CheA, putative (NCBI) 206, 266
GSU0330 GSU0330 general secretion pathway protein C, putative (NCBI) 173, 189
GSU0363 dinG ATP-dependent helicase DinG (NCBI) 107, 266
GSU0805 fsxA cytoplasmic membrane protein FsxA (NCBI) 232, 266
GSU0848 GSU0848 ferredoxin family protein, putative (VIMSS) 21, 189
GSU0875 GSU0875 hypothetical protein (VIMSS) 266, 291
GSU1015 GSU1015 hypothetical protein (VIMSS) 21, 189
GSU1035 GSU1035 methyl-accepting chemotaxis protein (NCBI) 57, 189
GSU1044 GSU1044 MutT/nudix family protein (VIMSS) 118, 266
GSU1065 GSU1065 hypothetical protein (VIMSS) 173, 189
GSU1085 GSU1085 hypothetical protein (VIMSS) 57, 189
GSU1142 cheW-3 purine-binding chemotaxis protein CheW (NCBI) 189, 241
GSU1163 GSU1163 ABC transporter, permease protein (VIMSS) 189, 266
GSU1220 GSU1220 response regulator (VIMSS) 189, 336
GSU1295 GSU1295 conserved hypothetical protein (VIMSS) 266, 293
GSU1395 GSU1395 hypothetical protein (VIMSS) 57, 189
GSU1533 recC exodeoxyribonuclease V, gamma subunit (NCBI) 45, 266
GSU1577 cobO cob(I)alamin adenosyltransferase (NCBI) 189, 231
GSU1942 GSU1942 UDP-glucose/GDP-mannose dehydrogenase family protein (VIMSS) 189, 319
GSU2013 GSU2013 phosphoglucomutase/phosphomannomutase family protein (VIMSS) 55, 189
GSU2118 GSU2118 integrative genetic element Gsu21, integrase (VIMSS) 189, 307
GSU2137 GSU2137 metal ion efflux outer membrane protein family protein, putative (VIMSS) 110, 189
GSU2175 GSU2175 trfA-related protein (VIMSS) 71, 189
GSU2296 GSU2296 HD domain protein (VIMSS) 141, 266
GSU2302 GSU2302 trehalose-phosphatase, putative (VIMSS) 20, 189
GSU2386 GSU2386 methylcobamide:CoM methyltransferase-related protein (NCBI) 189, 266
GSU2393 GSU2393 ISGsu5, transposase, truncation (VIMSS) 121, 189
GSU2460 GSU2460 ribonuclease BN, putative (VIMSS) 118, 266
GSU2534 GSU2534 sensory box/response regulator (VIMSS) 96, 266
GSU2559 GSU2559 exopolyphosphatase, putative (VIMSS) 266, 291
GSU2599 GSU2599 ISGsu4, transposase (VIMSS) 266, 268
GSU2719 hoxY NAD-reducing hydrogenase, delta subunit (NCBI) 189, 224
GSU2767 GSU2767 cytochrome c family protein, putative (NCBI) 107, 266
GSU2901 GSU2901 membrane protein, putative (VIMSS) 186, 266
GSU2933 GSU2933 cytochrome b/b6 complex, iron-sulfur subunit (VIMSS) 107, 266
GSU2934 GSU2934 cytochrome c family protein (NCBI) 45, 266
GSU2993 GSU2993 cobalamin biosynthesis protein CbiG, putative (NCBI) 266, 291
GSU3116 GSU3116 1-acyl-sn-glycerol-3-phosphate acyltransferase, putative (NCBI) 81, 189
GSU3153 GSU3153 iron-sulfur cluster-binding protein (VIMSS) 252, 266
GSU3198 cheY-7 chemotaxis protein CheY (NCBI) 189, 326
GSU3202 GSU3202 hypothetical protein (VIMSS) 189, 326
GSU3325 uvrA excinuclease ABC, A subunit (NCBI) 38, 266
GSU3364 GSU3364 hypothetical protein (VIMSS) 81, 189
GSU3428 GSU3428 cytochrome c family protein, putative (NCBI) 189, 318
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 GSU2386
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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