Organism : Geobacter sulfurreducens | Module List :
GSU2994 cobM

precorrin-4 C11-methyltransferase (NCBI)

CircVis
Functional Annotations (6)
Function System
Precorrin-4 methylase cog/ cog
cobalamin biosynthetic process go/ biological_process
precorrin-4 C11-methyltransferase activity go/ molecular_function
Porphyrin and chlorophyll metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
cobM_cbiF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2994
(Mouseover regulator name to see its description)

GSU2994 is regulated by 24 influences and regulates 0 modules.
Regulators for GSU2994 cobM (24)
Regulator Module Operator
GSU0013 156 tf
GSU0205 156 tf
GSU0399 156 tf
GSU0473 156 tf
GSU0735 156 tf
GSU0770 156 tf
GSU1410 156 tf
GSU1626 156 tf
GSU1989 156 tf
GSU2523 156 tf
GSU2587 156 tf
GSU2915 156 tf
GSU3387 156 tf
GSU0207 153 tf
GSU0514 153 tf
GSU0534 153 tf
GSU0551 153 tf
GSU0598 153 tf
GSU0735 153 tf
GSU0776 153 tf
GSU1095 153 tf
GSU1542 153 tf
GSU1586 153 tf
GSU2952 153 tf

Warning: GSU2994 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
2466 7.80e+03 tttCCt.ctgagttGc.GAta
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2467 3.60e+04 A.ATcGTttcC
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2472 3.30e+03 TgacGGgcCGttTtcccT
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2473 1.90e+04 GCat.TAaTtTAat.gGTTt
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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 GSU2994

GSU2994 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Precorrin-4 methylase cog/ cog
cobalamin biosynthetic process go/ biological_process
precorrin-4 C11-methyltransferase activity go/ molecular_function
Porphyrin and chlorophyll metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
cobM_cbiF tigr/ tigrfam
Module neighborhood information for GSU2994

GSU2994 has total of 42 gene neighbors in modules 153, 156
Gene neighbors (42)
Gene Common Name Description Module membership
GSU0237 GSU0237 MaoC-like domain protein (NCBI) 156, 333
GSU0365 cyd-2 cytochrome c3 (NCBI) 52, 156
GSU0370 GSU0370 hypothetical protein (VIMSS) 144, 156
GSU0376 gcvH-1 glycine cleavage system H protein (NCBI) 153, 296
GSU0377 GSU0377 glycine cleavage system P protein, subunit 1 (VIMSS) 153, 296
GSU0378 GSU0378 glycine cleavage system P protein, subunit 2 (VIMSS) 153, 296
GSU0379 GSU0379 biotin/lipoate A/B protein ligase family protein (NCBI) 153, 296
GSU0380 lipA lipoic acid synthetase (NCBI) 153, 296
GSU0382 GSU0382 conserved hypothetical protein (VIMSS) 153, 296
GSU0400 GSU0400 methyl-accepting chemotaxis protein (VIMSS) 82, 156
GSU0498 GSU0498 hypothetical protein (VIMSS) 153, 272
GSU0540 GSU0540 hypothetical protein (NCBI) 142, 156
GSU0750 GSU0750 methyl-accepting chemotaxis protein, putative (VIMSS) 25, 153
GSU0902 GSU0902 None 153, 272
GSU0970 GSU0970 conserved hypothetical protein (VIMSS) 153, 253
GSU0971 prfA peptidyl-tRNA hydrolase domain protein (NCBI) 153, 178
GSU1052 GSU1052 hydrolase, alpha/beta fold family (VIMSS) 122, 153
GSU1054 GSU1054 conserved hypothetical protein (VIMSS) 34, 153
GSU1055 GSU1055 membrane protein, putative (VIMSS) 78, 153
GSU1067 GSU1067 conserved hypothetical protein (VIMSS) 156, 183
GSU1322 ccdA cytochrome c biogenesis protein CcdA (NCBI) 153, 214
GSU1555 GSU1555 sensory box histidine kinase/response regulator (VIMSS) 153, 214
GSU1571 GSU1571 conserved domain protein (NCBI) 121, 153
GSU1704 GSU1704 methyl-accepting chemotaxis protein, putative (VIMSS) 156, 329
GSU1997 GSU1997 PDZ domain protein (NCBI) 156, 333
GSU2124 GSU2124 thioredoxin-related domain protein (VIMSS) 78, 153
GSU2157 nrd conserved domain protein (NCBI) 70, 153
GSU2161 GSU2161 hypothetical protein (VIMSS) 78, 153
GSU2340 GSU2340 Na+/H+ ion antiporter family protein (NCBI) 153, 225
GSU2364 rfbA mannose-6-phosphate isomerase (NCBI) 112, 156
GSU2464 GSU2464 hypothetical protein (VIMSS) 156, 183
GSU2565 GSU2565 sensor histidine kinase (VIMSS) 112, 156
GSU2588 lpdA-2 alpha keto acid dehydrogenase complex, E3 component, lipoamide dehydrogenase (NCBI) 75, 153
GSU2589 GSU2589 hypothetical protein (VIMSS) 156, 190
GSU2600 GSU2600 None 156, 333
GSU2651 GSU2651 amino acid ABC transporter, ATP-binding protein (VIMSS) 13, 156
GSU2862 GSU2862 None 156, 231
GSU2992 cobQ cobyric acid synthase (NCBI) 89, 153
GSU2994 cobM precorrin-4 C11-methyltransferase (NCBI) 153, 156
GSU3027 GSU3027 chemotaxis MotA protein (VIMSS) 153, 286
GSU3156 GSU3156 methyl-accepting chemotaxis protein, putative (VIMSS) 16, 153
GSU3162 GSU3162 L-allo-threonine aldolase (VIMSS) 148, 153
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 GSU2994
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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