Organism : Clostridium acetobutylicum | Module List :
CAC0086

Muconate cycloisomerase related protein, ortholog of YKGB B.subtilis (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
3-carboxymuconate cyclase cog/ cog
6-phosphogluconolactonase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0086
(Mouseover regulator name to see its description)

CAC0086 is regulated by 37 influences and regulates 0 modules.
Regulators for CAC0086 (37)
Regulator Module Operator
CAC0078 219 tf
CAC0191 219 tf
CAC0231 219 tf
CAC0422 219 tf
CAC0461 219 tf
CAC0493 219 tf
CAC0569 219 tf
CAC0681 219 tf
CAC0693 219 tf
CAC0929 219 tf
CAC1086 219 tf
CAC1536 219 tf
CAC2394 219 tf
CAC2851 219 tf
CAC2934 219 tf
CAC3224 219 tf
CAC3409 219 tf
CAC3647 219 tf
CAC3669 219 tf
CAC3731 219 tf
CAC0155 75 tf
CAC0422 75 tf
CAC0461 75 tf
CAC0569 75 tf
CAC0681 75 tf
CAC0929 75 tf
CAC1086 75 tf
CAC1404 75 tf
CAC1536 75 tf
CAC2851 75 tf
CAC2934 75 tf
CAC2966 75 tf
CAC3224 75 tf
CAC3349 75 tf
CAC3525 75 tf
CAC3647 75 tf
CAC3669 75 tf

Warning: CAC0086 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
6804 2.80e-05 AGGGgG
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6805 1.70e-02 GaaAaCgaTaac
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7090 5.10e-05 gaAgGGtG
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7091 2.10e+01 TGaaAaCGtT
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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 CAC0086

CAC0086 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
3-carboxymuconate cyclase cog/ cog
6-phosphogluconolactonase activity go/ molecular_function
Module neighborhood information for CAC0086

CAC0086 has total of 23 gene neighbors in modules 75, 219
Gene neighbors (23)
Gene Common Name Description Module membership
CAC0079 CAC0079 Hypothetical protein (NCBI ptt file) 219, 309
CAC0086 CAC0086 Muconate cycloisomerase related protein, ortholog of YKGB B.subtilis (NCBI ptt file) 75, 219
CAC0435 CAC0435 Hypothetical protein (NCBI ptt file) 75, 219
CAC0692 uxaC Glucuronate isomerase (NCBI ptt file) 75, 219
CAC0694 CAC0694 Permease of the Na+: galactoside symporter family (NCBI ptt file) 170, 219
CAC0804 CAC0804 Pectate lyase related protein, secreted (NCBI ptt file) 75, 219
CAC0834 CAC0834 Predicted integral membrane protein (NCBI ptt file) 75, 115
CAC1079 CAC1079 Uncharacterized protein, related to enterotoxins of other Clostridiales (NCBI ptt file) 75, 219
CAC1232 CAC1232 Predicted lytic murein transglycosylase (N-term. LysM motif repeat domain) (NCBI ptt file) 75, 219
CAC1405 bglA Beta-glucosidase (NCBI ptt file) 219, 321
CAC2252 CAC2252 Alpha-glucosidase fused to unknown alpha-amylase C-terminal. domain (NCBI ptt file) 75, 219
CAC2570 ganA Predicted arabinogalactan endo-1,4-beta-galactosidase (NCBI ptt file) 75, 170
CAC2729 CAC2729 Secreted protein containing SH3 domain homolog (NCBI ptt file) 75, 219
CAC2774 CAC2774 Methyl-accepting chemotaxis protein with HAMP domain (NCBI ptt file) 75, 219
CAC2891 CAC2891 Fusion of alpha-glucosidase (family 31 glycosyl hydrolase) and glycosidase (TreA/MalS family) (NCBI ptt file) 75, 219
CAC2959 galK Galactokinase (NCBI ptt file) 75, 219
CAC2960 GalE UDP-galactose 4-epimerase (NCBI ptt file) 75, 170
CAC2961 galT Galactose-1-phosphate uridyltransferase (NCBI ptt file) 75, 345
CAC3319 CAC3319 Signal transduction histidine kinase (NCBI ptt file) 29, 219
CAC3320 CAC3320 Predicted secreted protein homolog of yjcM/yhbB B.subtilis (NCBI ptt file) 75, 219
CAC3422 CAC3422 Sugar:proton symporter (possible xylulose) (NCBI ptt file) 75, 219
CAC3671 amyD ABC-type sugar transport system, permease component (NCBI ptt file) 75, 219
CAC3672 msmE ABC-type sugar transport system, periplasmic sugar-binding component (NCBI ptt file) 75, 219
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 CAC0086
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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