Organism : Clostridium acetobutylicum | Module List :
CAC0946

ComE-like protein, Metallo beta-lactamase superfamily hydrolase, secreted (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
Predicted hydrolase (metallo-beta-lactamase superfamily) cog/ cog
hydrolase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0946
(Mouseover regulator name to see its description)

CAC0946 is regulated by 10 influences and regulates 0 modules.
Regulators for CAC0946 (10)
Regulator Module Operator
CAC0144 44 tf
CAC0299 44 tf
CAC0763 44 tf
CAC0832 44 tf
CAC1536 44 tf
CAC1569 44 tf
CAC1869 44 tf
CAC2430 44 tf
CAC2476 44 tf
CAC2568 44 tf

Warning: CAC0946 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
6742 7.70e-03 aAAGGaG
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6743 5.30e+03 CA.g.caACaGgaAGCT
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7096 1.90e+01 CCatcTCC
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7097 2.70e+01 GgGGtg
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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 CAC0946

CAC0946 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted hydrolase (metallo-beta-lactamase superfamily) cog/ cog
hydrolase activity go/ molecular_function
Module neighborhood information for CAC0946

CAC0946 has total of 36 gene neighbors in modules 44, 222
Gene neighbors (36)
Gene Common Name Description Module membership
CAC0038 CAC0038 Hypothetical protein (NCBI ptt file) 44, 258
CAC0070 CAC0070 Hypothetical protein (NCBI ptt file) 44, 78
CAC0188 nagA N-acetylglucosamine-6-phosphate deacetylase (gene nagA) (NCBI ptt file) 44, 366
CAC0441 CAC0441 Uncharacterized conserved membrane protein of SANA family (NCBI ptt file) 14, 44
CAC0509 CAC0509 PHP family protein (NCBI ptt file) 44, 258
CAC0602 ftsH ATP-dependent zinc metallopeptidase FtsH (cell dividion protein) (NCBI ptt file) 91, 222
CAC0764 CAC0764 NADPH-dependent glutamate synthase beta chain (NCBI ptt file) 44, 91
CAC0946 CAC0946 ComE-like protein, Metallo beta-lactamase superfamily hydrolase, secreted (NCBI ptt file) 44, 222
CAC1539 CAC1539 Gamma-glutamylcysteine synthetase (NCBI ptt file) 109, 222
CAC1552 CAC1552 Response regulator (CheY-like receiver domain and HTH DNA-binding domain) (NCBI ptt file) 44, 366
CAC1626 CAC1626 Glycerol dehydrogenase (NCBI ptt file) 222, 238
CAC1637 CAC1637 Hypothetical protein, CF-12 family (NCBI ptt file) 44, 349
CAC1870 CAC1870 Hypothetical protein (NCBI ptt file) 44, 342
CAC1951 CAC1951 Site-specific recombinases, DNA invertase Pin homolog (NCBI ptt file) 44, 332
CAC2039 CAC2039 Hypothetical protein, CF-5 family (NCBI ptt file) 44, 190
CAC2434 CAC2434 Membrane associatehistidine kinase with HAMP domain (NCBI ptt file) 44, 312
CAC2436 CAC2436 Uncharacterized conserved membrane protein (NCBI ptt file) 44, 271
CAC2701 guaB IMP dehydrogenase (NCBI ptt file) 222, 328
CAC3012 CAC3012 ATPase component of ABC transporter, with duplicated ATPase domains (NCBI ptt file) 44, 84
CAC3194 murD UDP-N-acetylmuramoylalanine D-glutamate ligase (NCBI ptt file) 44, 142
CAC3220 CAC3220 Response regulator (CheY-like receiver domain and HTH-type DNA-binding domain) (NCBI ptt file) 44, 174
CAC3535 CAC3535 Type II restriction enzyme, methylase subunit (NCBI ptt file) 53, 222
CAC3536 CAC3536 Uncharacterized conserved protein, YbeA family (NCBI ptt file) 113, 222
CAC3570 accC Biotin carboxylase (NCBI ptt file) 44, 225
CAC3572 accB Biotin carboxyl carrier protein of acetyl-CoA carboxylase (NCBI ptt file) 44, 91
CAC3703 CAC3703 Hypothetical protein (NCBI ptt file) 44, 349
CAC3704 CAC3704 Hypothetical protein, CF-7 family (NCBI ptt file) 44, 356
CAC3705 CAC3705 Hypothetical protein, CF-37 family(almost identical) (NCBI ptt file) 44, 349
CAC3706 CAC3706 Hypothetical protein, CF-12 family (NCBI ptt file) 44, 349
CAC3707 CAC3707 Uncharacterized protein, homolog of Bacillus firmus (gi:2654481) (NCBI ptt file) 44, 349
CAC3708 CAC3708 Hypothetical protein (NCBI ptt file) 36, 44
CAC3709 CAC3709 DNA segregation ATPase, FtsK/SpoIIIE family, YUKA B.subtilis ortholog (NCBI ptt file) 36, 44
CAC3710 CAC3710 Uncharacterized protein, YUKC B.subtilis homolog (NCBI ptt file) 36, 44
CAC3711 CAC3711 Hypothetical protein (NCBI ptt file) 36, 44
CAC3712 CAC3712 Hypothetical protein (NCBI ptt file) 44, 356
CAC3713 CAC3713 Uncharacterized conserved protein, yukE/yfjA B.subtilis family (NCBI ptt file) 44, 349
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 CAC0946
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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