Organism : Clostridium acetobutylicum | Module List :
CAC1018

Predicted membrane protein (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
catalytic activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1018
(Mouseover regulator name to see its description)

CAC1018 is regulated by 20 influences and regulates 0 modules.
Regulators for CAC1018 (20)
Regulator Module Operator
CAC1046 287 tf
CAC1800 287 tf
CAC2473 287 tf
CAC2552 287 tf
CAC2568 287 tf
CAC3088 287 tf
CAC3507 287 tf
CAC3509 287 tf
CAC3611 287 tf
CAC1046 326 tf
CAC1340 326 tf
CAC1670 326 tf
CAC1719 326 tf
CAC2113 326 tf
CAC2476 326 tf
CAC2495 326 tf
CAC3324 326 tf
CAC3509 326 tf
CAC3579 326 tf
CAC3647 326 tf

Warning: CAC1018 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
7226 2.00e-02 .aGGtG
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7227 4.00e+04 cGTAATTcACATAAAaGGTc
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7304 5.30e+01 agGAGTGaac
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7305 3.00e+03 TA.AtgcTGca
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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 CAC1018

CAC1018 is enriched for 1 functions in 2 categories.
Enrichment Table (1)
Function System
catalytic activity go/ molecular_function
Module neighborhood information for CAC1018

CAC1018 has total of 40 gene neighbors in modules 287, 326
Gene neighbors (40)
Gene Common Name Description Module membership
CAC0237 CAC0237 ABC transporter, permease component (NCBI ptt file) 106, 287
CAC0291 CAC0291 FUSION: methionine sintase I (cobalamin dependent) and 5,10 methylenetetrahydrofolate reductase (NCBI ptt file) 259, 287
CAC0371 CAC0371 Response regulator (CheY-like domain and HTH domain) (NCBI ptt file) 71, 287
CAC0394 kdgA Deoxyphosphogluconate aldolase (gene kdgA) (NCBI ptt file) 83, 326
CAC0418 CAC0418 Predicted phosphatase, HAD family (NCBI ptt file) 261, 287
CAC0605 CAC0605 Predicted phosphatase (NCBI ptt file) 287, 356
CAC0607 CAC0607 Aspartyl aminopeptidase (NCBI ptt file) 287, 309
CAC0718 CAC0718 Ortholog ycnD B.subtilis, nitroreductase (NCBI ptt file) 83, 326
CAC0812 CAC0812 Pectate lyase related protein, secreted (NCBI ptt file) 108, 326
CAC1018 CAC1018 Predicted membrane protein (NCBI ptt file) 287, 326
CAC1046 CAC1046 Transcriptional regulator, LysR family (NCBI ptt file) 71, 287
CAC1145 CAC1145 Hypothetical protein (NCBI ptt file) 326, 344
CAC1161 CAC1161 Predicted ATPase of HSP70 class (NCBI ptt file) 187, 326
CAC1198 recJ Single-stranded-DNA-specific exonuclease (recJ) (NCBI ptt file) 187, 326
CAC1330 CAC1330 Metal-dependent hydrolases of the beta-lactamase superfamily, possible sulfatase (NCBI ptt file) 287, 356
CAC1424 CAC1424 Zn-dependent hydrolase, glyoxylase II family (NCBI ptt file) 287, 326
CAC1516 CAC1516 Response regulator (CheY-like receiver domain and HTH DNA-binding domain) (NCBI ptt file) 140, 287
CAC1548 trxB Thioredoxin reductase (NCBI ptt file) 227, 326
CAC1582 CAC1582 Membrane associated histidine kinase-like ATPase (NCBI ptt file) 259, 287
CAC1657 CAC1657 Uncharacterized conserved protein, yisX B.subtilis ortholog (NCBI ptt file) 279, 326
CAC1658 CAC1658 Phospholipase D family protein (NCBI ptt file) 73, 326
CAC1670 CAC1670 Response regulator (CheY-like receiver domain and DNA-binding HTH domain) (NCBI ptt file) 185, 326
CAC1671 CAC1671 Predicted ATPase related to the helicase subunit of the Holliday junction resolvase (NCBI ptt file) 291, 326
CAC1672 CAC1672 Rad3-related DNA helicase (NCBI ptt file) 291, 326
CAC1969 CAC1969 Possible plasmid transfer factor, TraK (NCBI ptt file) 287, 291
CAC1970 CAC1970 Hypothetical protein (NCBI ptt file) 185, 326
CAC2178 CAC2178 Predicted CDP-4-keto-6-deoxy-D-glucose-3-dehydrase (NCBI ptt file) 326, 336
CAC2472 CAC2472 Alpha/beta superfamily hydrolase (NCBI ptt file) 261, 287
CAC2495 CAC2495 Predicted transcriptional regulator (NCBI ptt file) 258, 326
CAC2545 CAC2545 Hypothetical protein (NCBI ptt file) 70, 326
CAC2684 CAC2684 Sugar kinase, ribokinase family (NCBI ptt file) 83, 326
CAC2735 CAC2735 Response regulator (CheY-like receiver domain and HTH-type DNA-binding) (NCBI ptt file) 74, 287
CAC2996 CAC2996 Superfamily II DNA/RNA helicase, SNF2 family (NCBI ptt file) 259, 287
CAC3088 CAC3088 NtrC family transcriptional regulator, ATPase domain fused to two PAS domains (NCBI ptt file) 113, 287
CAC3457 CAC3457 Predicted membrane protein (NCBI ptt file) 287, 356
CAC3478 CAC3478 Predicted membrane protein (NCBI ptt file) 207, 326
CAC3509 CAC3509 Transcriptional regulator, MerR family (duplicated domains) (NCBI ptt file) 287, 356
CAC3516 CAC3516 Membrane-associated histidine kinase with HAMP domain (NCBI ptt file) 261, 326
CAC3517 CAC3517 Response regulator (CheY-like receiver domain and HTH-type DNA-binding domain) (NCBI ptt file) 217, 326
CAC3587 CAC3587 DNA replication protein DnaD (NCBI ptt file) 13, 287
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 CAC1018
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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