Organism : Clostridium acetobutylicum | Module List :
CAC1086 xylR

Transcriptional regulators of NagC/XylR family (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
Transcriptional regulator/sugar kinase cog/ cog
glucokinase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1086
(Mouseover regulator name to see its description)

CAC1086 is regulated by 22 influences and regulates 11 modules.
Regulators for CAC1086 xylR (22)
Regulator Module Operator
CAC0155 340 tf
CAC0531 340 tf
CAC0859 340 tf
CAC0933 340 tf
CAC1086 340 tf
CAC1455 340 tf
CAC2053 340 tf
CAC2060 340 tf
CAC2768 340 tf
CAC3046 340 tf
CAC3504 340 tf
CAC3525 340 tf
CAC0019 133 tf
CAC0155 133 tf
CAC0531 133 tf
CAC0569 133 tf
CAC0859 133 tf
CAC1086 133 tf
CAC2254 133 tf
CAC3504 133 tf
CAC3525 133 tf
CAC3669 133 tf

Warning: CAC1086 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
6918 2.70e-04 AGgaGgtga
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6919 6.10e-03 atGtAAAcgtTaTca
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7332 1.30e-04 aGGgGgtg
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7333 1.00e+00 AtgAtA.CgTtTaCA
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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 CAC1086

CAC1086 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Transcriptional regulator/sugar kinase cog/ cog
glucokinase activity go/ molecular_function
Module neighborhood information for CAC1086

CAC1086 has total of 28 gene neighbors in modules 133, 340
Gene neighbors (28)
Gene Common Name Description Module membership
CAC0149 CAC0149 Hypothetical protein (NCBI ptt file) 133, 340
CAC0164 CAC0164 ABC transporter, ATP binding-protein (NCBI ptt file) 133, 340
CAC0165 CAC0165 Predicted ABC transporter, permease component (NCBI ptt file) 133, 340
CAC0434 CAC0434 Putative enzyme of deoxyxylulose pathway (terpenoid biosinthesis), YgbB family, similar to yacN B.subtilis (NCBI ptt file) 133, 340
CAC1075 CAC1075 Beta-glucosidase family protein (NCBI ptt file) 133, 340
CAC1080 CAC1080 Uncharacterized protein, probably surface-located (NCBI ptt file) 170, 340
CAC1081 CAC1081 Uncharacterized protein, probably surface-located (NCBI ptt file) 133, 340
CAC1084 CAC1084 Beta-glucosidase family protein (NCBI ptt file) 133, 340
CAC1085 CAC1085 Alpha-glucosidase (NCBI ptt file) 133, 340
CAC1086 xylR Transcriptional regulators of NagC/XylR family (NCBI ptt file) 133, 340
CAC1231 CAC1231 Predicted dehydrogenase, YULF B.subtilis ortholog (NCBI ptt file) 133, 340
CAC1319 glpF Glycerol uptake facilitator protein, GLPF (NCBI ptt file) 4, 133
CAC1339 araE Possible sugar-proton symporter (NCBI ptt file) 133, 340
CAC1406 CAC1406 Transcriptional antiterminator (BglG family) (NCBI ptt file) 86, 133
CAC1454 CAC1454 Membrane associated histidine kinase-like ATPase (NCBI ptt file) 204, 340
CAC1455 CAC1455 Two-component system regulator (CheY domain and HTH-like DNA-binding domain) (NCBI ptt file) 204, 340
CAC1456 CAC1456 Sugar-binding periplasmic protein (NCBI ptt file) 204, 340
CAC2020 moeA Molybdopterin biosynthesis enzyme, MoeA, fused to molibdopterin-binding domain (NCBI ptt file) 133, 340
CAC2021 moeA Molybdopterin biosynthesis enzyme, MoeA (short form) (NCBI ptt file) 133, 209
CAC2512 CAC2512 Hypothetical protein (NCBI ptt file) 133, 270
CAC2610 CAC2610 L-fucose isomerase related protein (NCBI ptt file) 12, 340
CAC2611 CAC2611 Hypothetical protein (NCBI ptt file) 12, 340
CAC2612 xylB Xylulose kinase (NCBI ptt file) 12, 340
CAC2806 CAC2806 Predicted phosphohydrolase, Icc family (NCBI ptt file) 133, 340
CAC2807 CAC2807 Endo-1,3(4)-beta-glucanase family 16 (NCBI ptt file) 133, 340
CAC2809 CAC2809 Predicted HD superfamily hydrolase (NCBI ptt file) 133, 340
CAC3425 glvC PTS system, (possibly glucose-specific) IIBC component (NCBI ptt file) 133, 170
CAC3670 amyC Sugar permease (NCBI ptt file) 133, 340
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 CAC1086
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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