Organism : Clostridium acetobutylicum | Module List :
CAC2517 nrpE

Extracellular neutral metalloprotease, NPRE (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Zinc metalloprotease (elastase) cog/ cog
metalloendopeptidase activity go/ molecular_function
extracellular region go/ cellular_component
proteolysis go/ biological_process
zinc ion binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2517
(Mouseover regulator name to see its description)

CAC2517 is regulated by 26 influences and regulates 0 modules.
Regulators for CAC2517 nrpE (26)
Regulator Module Operator
CAC0360 305 tf
CAC0821 305 tf
CAC1426 305 tf
CAC1467 305 tf
CAC1509 305 tf
CAC1578 305 tf
CAC2209 305 tf
CAC2254 305 tf
CAC2259 305 tf
CAC2306 305 tf
CAC2955 305 tf
CAC3496 305 tf
CAC3509 305 tf
CAC3695 305 tf
CAC0189 269 tf
CAC0289 269 tf
CAC0681 269 tf
CAC1689 269 tf
CAC1696 269 tf
CAC2242 269 tf
CAC2306 269 tf
CAC2307 269 tf
CAC3142 269 tf
CAC3646 269 tf
CAC3649 269 tf
CAC3729 269 tf

Warning: CAC2517 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
7190 4.80e-06 GGggGat
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7191 6.80e+03 AccTTTttTGg
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7262 4.30e+00 AGg.GG
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7263 2.30e+02 CcCCCC
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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 CAC2517

CAC2517 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Zinc metalloprotease (elastase) cog/ cog
metalloendopeptidase activity go/ molecular_function
extracellular region go/ cellular_component
proteolysis go/ biological_process
zinc ion binding go/ molecular_function
Module neighborhood information for CAC2517

CAC2517 has total of 34 gene neighbors in modules 269, 305
Gene neighbors (34)
Gene Common Name Description Module membership
CAC0014 CAC0014 Aminotransferase (NCBI ptt file) 250, 305
CAC0092 CAC0092 Uncharacterized predicted membrane protein, YTWI B.subtilis ortholog (NCBI ptt file) 305, 363
CAC0353 CAC0353 2,3-cyclic-nucleotide 2'phosphodiesterase (duplication) (NCBI ptt file) 42, 269
CAC0668 CAC0668 Predicted membrane protein (NCBI ptt file) 174, 305
CAC0746 CAC0746 Secreted protease metal-dependent protease (NCBI ptt file) 269, 345
CAC0824 CAC0824 Thioredoxin (NCBI ptt file) 305, 334
CAC1509 CAC1509 Specialized sigma subunit of RNA polymerase (NCBI ptt file) 305, 367
CAC1510 CAC1510 Hypothetical protein (NCBI ptt file) 293, 305
CAC1609 CAC1609 Zn-finger containing protein (NCBI ptt file) 293, 305
CAC1674 gltB Small subunit of NADPH-dependent glutamate synthase (NCBI ptt file) 29, 269
CAC1751 smc Chromosome segregation SMC protein, ATPase (NCBI ptt file) 213, 269
CAC1752 ftsY Signal recognition particle GTPase, FtsY (NCBI ptt file) 29, 269
CAC1811 CAC1811 Periplasmic serine protease, YMFB B.subtilis ortholog (NCBI ptt file) 142, 269
CAC1812 CAC1812 Sporulation protein SpoIIIE, DNA segregation ATPase (NCBI ptt file) 29, 269
CAC1841 CAC1841 Uncharacterized protein, related to Spore coat protein CotS (NCBI ptt file) 73, 269
CAC2238 glgC ADP-glucose pyrophosphorylase (NCBI ptt file) 42, 269
CAC2239 glgA Glycogen synthase, glgA (NCBI ptt file) 42, 269
CAC2507 CAC2507 Predicted membrane protein (NCBI ptt file) 29, 269
CAC2517 nrpE Extracellular neutral metalloprotease, NPRE (NCBI ptt file) 269, 305
CAC2623 CAC2623 Possible sensorory transduction protein, containing AAA ATPase domain, TPR repeats domain, GGDEF domain and GAF domain (NCBI ptt file) 134, 269
CAC3169 ilvB Acetolactate synthase large subunit (NCBI ptt file) 305, 334
CAC3170 ilvD Dihydroxy-acid dehydratase (NCBI ptt file) 305, 334
CAC3171 leuB Isopropylmalate dehydrogenase (NCBI ptt file) 305, 334
CAC3172 leuD 3-isopropylmalate dehydratase, small subunit (NCBI ptt file) 305, 334
CAC3173 leuC 3-Isopropylmalate dehydratase, large subunit (NCBI ptt file) 305, 334
CAC3174 leuA 2-isopropylmalate synthase (NCBI ptt file) 305, 334
CAC3633 CAC3633 Hypothetical protein (NCBI ptt file) 42, 269
CAC3634 CAC3634 Oligopeptide ABC transporter, periplasmic substrate-binding component (NCBI ptt file) 42, 269
CAC3635 CAC3635 Oligopeptide ABC transporter, ATPase component (NCBI ptt file) 42, 269
CAC3636 CAC3636 Oligopeptide ABC transporter, ATPase component (NCBI ptt file) 42, 269
CAC3637 CAC3637 Oligopeptide ABC transporter, permease component (NCBI ptt file) 42, 269
CAC3638 CAC3638 Oligopeptide ABC transporter, permease component (NCBI ptt file) 42, 269
CAC3639 CAC3639 CRO repressor-like DNA-binding protein (NCBI ptt file) 42, 269
CAC3646 CAC3646 Predicted transcriptional regulator, containing DNA-binding domain of xre family (NCBI ptt file) 60, 269
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 CAC2517
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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