Organism : Clostridium acetobutylicum | Module List :
CAC0178 appC

Oligopeptide transport permease protein (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
ABC-type dipeptide/oligopeptide/nickel transport systems, permease components cog/ cog
transport go/ biological_process
nickel-transporting ATPase activity go/ molecular_function
membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0178
(Mouseover regulator name to see its description)

CAC0178 is regulated by 25 influences and regulates 0 modules.
Regulators for CAC0178 appC (25)
Regulator Module Operator
CAC0768 278 tf
CAC0860 278 tf
CAC0951 278 tf
CAC1670 278 tf
CAC1695 278 tf
CAC2084 278 tf
CAC2306 278 tf
CAC2307 278 tf
CAC2471 278 tf
CAC2768 278 tf
CAC3216 278 tf
CAC3443 278 tf
CAC3673 278 tf
CAC0144 314 tf
CAC0183 314 tf
CAC0191 314 tf
CAC0461 314 tf
CAC0763 314 tf
CAC0849 314 tf
CAC1786 314 tf
CAC2546 314 tf
CAC2773 314 tf
CAC3046 314 tf
CAC3142 314 tf
CAC3424 314 tf

Warning: CAC0178 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
7208 2.70e-05 aaGgggGa
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7209 4.60e+04 aCGGGA
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7280 2.00e+04 CcAGTC
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7281 3.50e+01 gggAGGATgA
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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 CAC0178

CAC0178 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
ABC-type dipeptide/oligopeptide/nickel transport systems, permease components cog/ cog
transport go/ biological_process
nickel-transporting ATPase activity go/ molecular_function
membrane go/ cellular_component
Module neighborhood information for CAC0178

CAC0178 has total of 37 gene neighbors in modules 278, 314
Gene neighbors (37)
Gene Common Name Description Module membership
CAC0003 CAC0003 Small conserved protein, ortholog of YAAA B.subtilis (NCBI ptt file) 105, 278
CAC0007 gyrA DNA gyrase (topoisomerase II) A subunit (NCBI ptt file) 29, 278
CAC0111 CAC0111 Glutamine-binding periplasmic protein fused to glutamine permease (NCBI ptt file) 106, 278
CAC0177 appB Oligopeptide transport permease protein (NCBI ptt file) 314, 345
CAC0178 appC Oligopeptide transport permease protein (NCBI ptt file) 278, 314
CAC0179 appD Oligopeptide transport ATP-binding protein (NCBI ptt file) 314, 366
CAC0180 appF Oligopeptide ABC transporter, ATP-binding protein (NCBI ptt file) 179, 278
CAC0181 CAC0181 Similar to beta-lactamase (NCBI ptt file) 314, 320
CAC0184 CAC0184 Predicted acetyltransferase (NCBI ptt file) 236, 314
CAC0185 CAC0185 Uncharacterized membrane protein, YBBC B.subtilis ortholog (NCBI ptt file) 115, 314
CAC0285 CAC0285 DNA-damage repair protein, dinP/uvrX ortholog (NCBI ptt file) 271, 314
CAC0627 CAC0627 Transcriptional regulator, MarR/EmrR family (NCBI ptt file) 278, 283
CAC0655 CAC0655 Hypothetical protein, CF-26 family (NCBI ptt file) 278, 318
CAC0702 CAC0702 Predicted lipoprotein, Med/BMP family (NCBI ptt file) 58, 278
CAC0714 secG Membrane protein secG involved in protein secretion (NCBI ptt file) 25, 278
CAC0769 CAC0769 Uncharacterized conserved protein (NCBI ptt file) 118, 314
CAC0793 CAC0793 Uncharacterized conserved protein of probably eukaryotic origin (NCBI ptt file) 279, 314
CAC1453 rbsB Ribose ABC transporter (ribose-binding periplasmic component) (NCBI ptt file) 235, 278
CAC1467 CAC1467 Transcriptional regulator, Lrp family (NCBI ptt file) 178, 278
CAC1542 CAC1542 Predicted membrane protein (NCBI ptt file) 278, 283
CAC1728 CAC1728 Serine/threonine protein kinase, Pkn2 family (YLOP B.subtilis ortholog) (NCBI ptt file) 314, 329
CAC1731 CAC1731 Predicted nucleotide-binding protein, YLOS B.subtilis ortholog (NCBI ptt file) 2, 278
CAC1750 CAC1750 SpoVS-related protein (NCBI ptt file) 29, 278
CAC1968 CAC1968 Pectate lyase related enzyme (NCBI ptt file) 174, 314
CAC2261 CAC2261 HD-hydrolase domain containing protein, YHAM B.subtilis ortholog (NCBI ptt file) 38, 278
CAC2263 addB ATP-dependent exonuclease synthesis protein AddB (superfamily I helicase) (NCBI ptt file) 159, 314
CAC2288 CAC2288 Acyl-protein synthetase, luxE (NCBI ptt file) 166, 314
CAC2306 CAC2306 Sporulation-specific sigma factor F (NCBI ptt file) 164, 278
CAC2307 CAC2307 Sigma factor F inhibitor spoIIAB (anti-sigma factor) (NCBI ptt file) 164, 278
CAC2321 CAC2321 Predicted glycosyltransferase (NCBI ptt file) 63, 278
CAC2635 CAC2635 Hypothetical protein (NCBI ptt file) 80, 278
CAC2724 CAC2724 Hypothetical protein (NCBI ptt file) 51, 278
CAC2727 CAC2727 Predicted PHP family hydrolase (NCBI ptt file) 53, 278
CAC2854 recD ATP-dependent exoDNAse (exonuclease V), alpha subunit, RecD (NCBI ptt file) 278, 286
CAC3342 CAC3342 Dehydrogenase related to 3-hydroxyisobutyrate dehydrogenase, YKWC B.subtilis ortholog (NCBI ptt file) 221, 314
CAC3373 CAC3373 Pectin methylesterase (NCBI ptt file) 206, 314
CAC3436 CAC3436 Probable alpha-arabinofuranosidase (NCBI ptt file) 314, 366
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 CAC0178
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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