Organism : Clostridium acetobutylicum | Module List :
CAC3164

Lysine-specific permease (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Amino acid transporters cog/ cog
succinate dehydrogenase activity go/ molecular_function
amino acid transport go/ biological_process
amino acid transmembrane transporter activity go/ molecular_function
integral to membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3164
(Mouseover regulator name to see its description)

CAC3164 is regulated by 23 influences and regulates 0 modules.
Regulators for CAC3164 (23)
Regulator Module Operator
CAC0310 265 tf
CAC0876 265 tf
CAC1280 265 tf
CAC1469 265 tf
CAC2495 265 tf
CAC3063 265 tf
CAC3200 265 tf
CAC3214 265 tf
CAC3429 265 tf
CAC3507 265 tf
CAC3677 265 tf
CAC3731 265 tf
CAC0093 301 tf
CAC1280 301 tf
CAC1467 301 tf
CAC1867 301 tf
CAC2306 301 tf
CAC2605 301 tf
CAC2955 301 tf
CAC3271 301 tf
CAC3466 301 tf
CAC3651 301 tf
CAC3677 301 tf

Warning: CAC3164 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
7182 4.30e-07 aAGGGgga
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7183 1.90e+04 CGAGGaG
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7254 1.30e+00 AAaacagGagGggt
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7255 3.40e+04 GTccACG
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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 CAC3164

CAC3164 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Amino acid transporters cog/ cog
succinate dehydrogenase activity go/ molecular_function
amino acid transport go/ biological_process
amino acid transmembrane transporter activity go/ molecular_function
integral to membrane go/ cellular_component
Module neighborhood information for CAC3164

CAC3164 has total of 48 gene neighbors in modules 265, 301
Gene neighbors (48)
Gene Common Name Description Module membership
CAC0093 CAC0093 Transcriptional regulators, LysR family (NCBI ptt file) 216, 301
CAC0152 CAC0152 Ribosomal-protein-alanine acetyltransferase (acetylating enzyme for N-terminal of ribosomal protein S5) (NCBI ptt file) 265, 285
CAC0154 MtlA PTS system, mannitol-specific IIBC component (gene MtlA) (NCBI ptt file) 301, 342
CAC0332 manB Beta-mannanase (NCBI ptt file) 191, 301
CAC0388 CAC0388 Hypothetical protein (NCBI ptt file) 301, 361
CAC0534 pps Phosphoenolpyruvate synthase (gene pps) (NCBI ptt file) 65, 301
CAC0561 CAC0561 Cellulase CelE ortholog; dockerin domain (NCBI ptt file) 43, 265
CAC0596 gerKA Spore germination protein. gerKA (NCBI ptt file) 230, 265
CAC0695 CAC0695 Altronate oxidoreductase (NCBI ptt file) 170, 301
CAC1140 CAC1140 Hypothetical protein (NCBI ptt file) 16, 301
CAC1290 CAC1290 Uncharacterized protein, homolog of YQFC B.subtilis (NCBI ptt file) 22, 265
CAC1291 CAC1291 Uncharacterized protein, YQFD ortholog, related spoIV gene product (NCBI ptt file) 22, 265
CAC1477 CAC1477 Hypothetical protein (NCBI ptt file) 272, 301
CAC1526 CAC1526 Amidase, related to GSP of E.coli (NCBI ptt file) 26, 301
CAC1541 CAC1541 Hypothetical protein, CF-36 family (NCBI ptt file) 200, 265
CAC1543 CAC1543 Lactate dehydrogenase (NCBI ptt file) 117, 265
CAC1553 CAC1553 Membrane associated sensory transduction histidine kinase (with HAMP domain) (NCBI ptt file) 41, 265
CAC1608 CAC1608 HIT family hydrolase (NCBI ptt file) 49, 265
CAC1620 CAC1620 Small acid-soluble spore protein (NCBI ptt file) 251, 265
CAC1676 CAC1676 Uncharacterized conserved protein (NCBI ptt file) 301, 332
CAC1867 CAC1867 Transcriptional regulator (phage-related) (Xre family) (NCBI ptt file) 301, 342
CAC2247 CAC2247 Site-specific recombinase, DNA invertase Pin homolog (NCBI ptt file) 270, 301
CAC2304 SpoVAD Stage V sporulation AD, SpoVAD (NCBI ptt file) 22, 265
CAC2509 CAC2509 Predicted acetyltransferase (NCBI ptt file) 165, 301
CAC2539 CAC2539 Predicted acetyltransferase (NCBI ptt file) 240, 265
CAC2540 CAC2540 Co/Zn/Cd efflux system component (NCBI ptt file) 207, 301
CAC2542 CAC2542 FAD/FMN-containing dehydrogenase (NCBI ptt file) 41, 265
CAC2600 CAC2600 Predicted membrane protein (NCBI ptt file) 300, 301
CAC2822 CAC2822 TPR-repeat-containing protein (NCBI ptt file) 165, 301
CAC3030 CAC3030 Hypothetical protein (NCBI ptt file) 41, 265
CAC3164 CAC3164 Lysine-specific permease (NCBI ptt file) 265, 301
CAC3237 msmX Multiple sugar-binding ABC-transporter, MSMX ATP-binding protein (NCBI ptt file) 301, 312
CAC3241 CAC3241 Uncharacterized conserved membrane protein, YYAD B.subtilis ortholog (NCBI ptt file) 150, 301
CAC3242 CAC3242 Uncharacterized Fe-S protein, PflX (pyruvate formate lyase activating protein) homolog (NCBI ptt file) 72, 301
CAC3261 ada Methylated DNA-protein cysteine methyltransferase (NCBI ptt file) 240, 265
CAC3274 CAC3274 Possible surface protein, responsible for cell interaction; contains cell adhesion domain and ChW-repeats (NCBI ptt file) 22, 265
CAC3333 CAC3333 Uncharacterized conserved protein, related to pyruvate formate-lyase activating enzyme (NCBI ptt file) 265, 285
CAC3451 CAC3451 Sugar/Na+(H+) simporter (NCBI ptt file) 170, 301
CAC3468 uvrC Excinuclease ABC, subunit C (uvrC) (NCBI ptt file) 207, 301
CAC3471 CAC3471 GMP reductase (NCBI ptt file) 223, 301
CAC3490 CAC3490 DNA gyrase inhibitory protein, GyrI (NCBI ptt file) 205, 301
CAC3507 CAC3507 Transcriptional regulator, MerR family (NCBI ptt file) 236, 265
CAC3543 CAC3543 Predicted membrane protein (NCBI ptt file) 265, 320
CAC3590 CAC3590 Predicted flavoprotein, YhiN family (NCBI ptt file) 174, 301
CAC3644 CAC3644 Oligopeptide ABC transporter, permease component (NCBI ptt file) 217, 301
CAC3659 CAC3659 S-adenosylmethionine-dependent methyltransferase (NCBI ptt file) 165, 265
CAC3680 kdpC/atkC K+-transporting ATPase, c chain (NCBI ptt file) 22, 265
CAC3682 kdpA/atkA K+-transporting ATPase, a chain (NCBI ptt file) 22, 265
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 CAC3164
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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