Organism : Clostridium acetobutylicum | Module List :
CAC0444 napA

Na/H antiporter (napA) (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Kef-type K+ transport systems, membrane components cog/ cog
regulation of pH go/ biological_process
solute:hydrogen antiporter activity go/ molecular_function
integral to membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0444
(Mouseover regulator name to see its description)

CAC0444 is regulated by 26 influences and regulates 0 modules.
Regulators for CAC0444 napA (26)
Regulator Module Operator
CAC0195 174 tf
CAC0681 174 tf
CAC0841 174 tf
CAC1430 174 tf
CAC1509 174 tf
CAC1696 174 tf
CAC2616 174 tf
CAC2859 174 tf
CAC2950 174 tf
CAC3143 174 tf
CAC3370 174 tf
CAC3418 174 tf
CAC3481 174 tf
CAC0023 62 tf
CAC0195 62 tf
CAC0859 62 tf
CAC0863 62 tf
CAC1430 62 tf
CAC1536 62 tf
CAC1578 62 tf
CAC2254 62 tf
CAC2934 62 tf
CAC3166 62 tf
CAC3418 62 tf
CAC3466 62 tf
CAC3504 62 tf

Warning: CAC0444 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
6778 4.90e-04 GgAGGt
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6779 3.30e+02 GGagaagG
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7000 3.00e-03 gttaAGGaGg
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7001 1.70e+03 GGaGTG
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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 CAC0444

CAC0444 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Kef-type K+ transport systems, membrane components cog/ cog
regulation of pH go/ biological_process
solute:hydrogen antiporter activity go/ molecular_function
integral to membrane go/ cellular_component
Module neighborhood information for CAC0444

CAC0444 has total of 45 gene neighbors in modules 62, 174
Gene neighbors (45)
Gene Common Name Description Module membership
CAC0009 CAC0009 Uncharacterized conserved protein, ortholog of YRXA B.subtilis (NCBI ptt file) 62, 312
CAC0134 CAC0134 Hypothetical protein, CF-19 family (NCBI ptt file) 62, 247
CAC0146 CAC0146 Related to ABC transporter permease component (NCBI ptt file) 62, 142
CAC0147 CAC0147 ABC transporter, ATP-binding protein (NCBI ptt file) 62, 142
CAC0193 CAC0193 Uncharacterized conserved membrane protein, affecting LPS biosynthesis (NCBI ptt file) 7, 174
CAC0194 CAC0194 Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file) 7, 174
CAC0205 CAC0205 Predicted phosphohydrolases, Icc family (NCBI ptt file) 62, 279
CAC0440 CAC0440 Homolog of osmotically induced OSMY protein of E.coli (NCBI ptt file) 62, 207
CAC0444 napA Na/H antiporter (napA) (NCBI ptt file) 62, 174
CAC0467 CAC0467 Uncharacterized membrane protein, homolog of YDAH B.subtilis (NCBI ptt file) 78, 174
CAC0492 CAC0492 Alanine racemase (NCBI ptt file) 174, 318
CAC0668 CAC0668 Predicted membrane protein (NCBI ptt file) 174, 305
CAC0678 CAC0678 CBS domains (NCBI ptt file) 160, 174
CAC0704 CAC0704 Sugar ABC transporter, permease protein (NCBI ptt file) 95, 174
CAC0738 CAC0738 DNA polymerase III epsilon subunit (3'-5' exonuclease) containing BRCT domain (NCBI ptt file) 62, 142
CAC0750 CAC0750 Hypothetical protein (NCBI ptt file) 62, 342
CAC0779 CAC0779 Amidase related to nicotinamidase (NCBI ptt file) 39, 62
CAC0840 potA Spermidine/putrescine ABC transporter, ATP-binding component (NCBI ptt file) 153, 174
CAC0934 CAC0934 Hypothetical protein (NCBI ptt file) 62, 177
CAC1019 CAC1019 Phospholipase C related protein (NCBI ptt file) 62, 80
CAC1238 CAC1238 Hypothetical protein (NCBI ptt file) 62, 348
CAC1468 CAC1468 Predicted acetyltransferase (NCBI ptt file) 174, 315
CAC1588 CAC1588 Malolactic regulator, LysR family (NCBI ptt file) 174, 366
CAC1696 sigG Specialized DNA-dependent RNA polymerase sigma subunit (NCBI ptt file) 174, 235
CAC1860 CAC1860 Predicted flavodoxin oxidoreductase (NCBI ptt file) 62, 312
CAC1968 CAC1968 Pectate lyase related enzyme (NCBI ptt file) 174, 314
CAC2431 CAC2431 Alkaline phosphatase superfamily enzyme (NCBI ptt file) 62, 312
CAC2438 CAC2438 Predicted phosphatase (NCBI ptt file) 174, 300
CAC2682 CAC2682 Hypothetical protein (NCBI ptt file) 62, 300
CAC2683 cotF Related to spore coat protein F (NCBI ptt file) 62, 300
CAC2776 CAC2776 Hypothetical protein (NCBI ptt file) 62, 102
CAC2781 CAC2781 Hypothetical protein (NCBI ptt file) 62, 345
CAC2875 tagO Undecaprenyl-phosphate (NCBI ptt file) 174, 235
CAC2938 CAC2938 Hypothetical protein (NCBI ptt file) 5, 62
CAC3032 CAC3032 Galactose mutarotase related enzyme (NCBI ptt file) 174, 315
CAC3168 CAC3168 Predicted membrane protein (NCBI ptt file) 62, 344
CAC3220 CAC3220 Response regulator (CheY-like receiver domain and HTH-type DNA-binding domain) (NCBI ptt file) 44, 174
CAC3230 CAC3230 Hydrogenase subunit (ferredoxin) (NCBI ptt file) 174, 330
CAC3232 CAC3232 Hypothetical protein (NCBI ptt file) 62, 247
CAC3357 CAC3357 Hypothetical protein (NCBI ptt file) 118, 174
CAC3379 CAC3379 Uncharacterized protein, YQFW B.subtilis homolog (NCBI ptt file) 62, 361
CAC3392 CAC3392 NADH-dependent butanol dehydrogenase (NCBI ptt file) 62, 91
CAC3504 CAC3504 Transcriptional regulator, AcrR family (NCBI ptt file) 62, 235
CAC3590 CAC3590 Predicted flavoprotein, YhiN family (NCBI ptt file) 174, 301
CAC3601 CAC3601 Nudix (MutT) family hydrolase (NCBI ptt file) 62, 259
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 CAC0444
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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