Organism : Clostridium acetobutylicum | Module List :
CAC3055

Sugar kinase (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
Predicted kinase related to galactokinase and mevalonate kinase cog/ cog
mevalonate kinase activity go/ molecular_function
ATP binding go/ molecular_function
cytoplasm go/ cellular_component
kinase activity go/ molecular_function
phosphorylation go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3055
(Mouseover regulator name to see its description)

CAC3055 is regulated by 19 influences and regulates 0 modules.
Regulators for CAC3055 (19)
Regulator Module Operator
CAC0265 48 tf
CAC0289 48 tf
CAC0461 48 tf
CAC1467 48 tf
CAC2306 48 tf
CAC2773 48 tf
CAC3046 48 tf
CAC3424 48 tf
CAC3649 48 tf
CAC3731 48 tf
CAC0189 323 tf
CAC0289 323 tf
CAC0457 323 tf
CAC0707 323 tf
CAC1467 323 tf
CAC3046 323 tf
CAC3409 323 tf
CAC3649 323 tf
CAC3729 323 tf

Warning: CAC3055 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
6750 8.20e-02 ga.AAgGGaG
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6751 1.10e+03 ccTtCGcC
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7298 4.60e+01 actcaAaTgaaatgAAAtgtG
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7299 1.60e+03 AAaCTgAaAag.Aggg
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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 CAC3055

CAC3055 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Predicted kinase related to galactokinase and mevalonate kinase cog/ cog
mevalonate kinase activity go/ molecular_function
ATP binding go/ molecular_function
cytoplasm go/ cellular_component
kinase activity go/ molecular_function
phosphorylation go/ biological_process
Module neighborhood information for CAC3055

CAC3055 has total of 24 gene neighbors in modules 48, 323
Gene neighbors (24)
Gene Common Name Description Module membership
CAC0432 CAC0432 Methyl-accepting chemotaxis protein (NCBI ptt file) 48, 319
CAC0462 CAC0462 Protein of short-chain alcohol dehydrogenase family (NCBI ptt file) 48, 224
CAC1410 CAC1410 Uncharacterized protein with repeats, similar to YCEG B.subtilis (NCBI ptt file) 34, 48
CAC1411 CAC1411 Similar to toxic anion resistance protein terA, ortholog of YCEH B.subtilis (NCBI ptt file) 48, 126
CAC1412 cdrC Methyl methane sulfonate/mytomycin C/UV resistance protein, GSP18 (YCEE) B.subtilis ortholog, TerE family protein (NCBI ptt file) 34, 48
CAC1413 CAC1413 Similar to C-terminal fragment of toxic anion resistance protein terA (NCBI ptt file) 48, 126
CAC1560 CAC1560 Hypothetical protein (NCBI ptt file) 48, 242
CAC1561 CAC1561 Glycosyltransferases, involved in cell wall biogenesis (NCBI ptt file) 242, 323
CAC1562 CAC1562 Predicted membrane protein (NCBI ptt file) 242, 323
CAC1563 CAC1563 Endoglucanase (fragment) (NCBI ptt file) 242, 323
CAC1564 CAC1564 Closely related to alginate O-acetylation protein (algI) (NCBI ptt file) 156, 323
CAC1565 CAC1565 Predicted membrane protein (NCBI ptt file) 156, 323
CAC1566 CAC1566 Diguanylate cyclase/phosphodiesterase domain 1 (GGDEF) (NCBI ptt file) 156, 323
CAC2490 CAC2490 Xre family DNA-binding domain and TPR repeats containing protein (NCBI ptt file) 48, 319
CAC3042 CAC3042 O-actetyl transferase related protein (NCBI ptt file) 48, 319
CAC3043 CAC3043 CPSC/CAPB subfamily ATPase (NCBI ptt file) 48, 319
CAC3044 CAC3044 CPSD/CAPA conserved membrane protein of Rol/Cld family (NCBI ptt file) 9, 48
CAC3053 CAC3053 Histidinol phosphatase related enzyme (NCBI ptt file) 9, 323
CAC3054 CAC3054 Phosphoheptose isomerase (NCBI ptt file) 156, 323
CAC3055 CAC3055 Sugar kinase (NCBI ptt file) 48, 323
CAC3056 CAC3056 Nucleoside-diphosphate-sugar pyrophosphorylase (NCBI ptt file) 9, 323
CAC3058 CAC3058 Mannose-1-phosphate guanylyltransferase (NCBI ptt file) 9, 323
CAC3059 CAC3059 Sugar transferases (NCBI ptt file) 9, 48
CAC3388 CAC3388 Methyl-accepting chemotaxis protein (NCBI ptt file) 48, 96
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 CAC3055
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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