Organism : Clostridium acetobutylicum | Module List :
CAC3247

Predicted transcriptional regulator, lacI/xre family (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3247
(Mouseover regulator name to see its description)

CAC3247 is regulated by 18 influences and regulates 10 modules.
Regulators for CAC3247 (18)
Regulator Module Operator
CAC0144 151 tf
CAC0265 151 tf
CAC0849 151 tf
CAC1559 151 tf
CAC1766 151 tf
CAC2675 151 tf
CAC3247 151 tf
CAC3731 151 tf
CAC0708 359 tf
CAC0832 359 tf
CAC1578 359 tf
CAC1695 359 tf
CAC1869 359 tf
CAC2254 359 tf
CAC2306 359 tf
CAC3166 359 tf
CAC3247 359 tf
CAC3518 359 tf

Warning: CAC3247 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
6954 8.40e-06 TgGAGGTG
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6955 1.00e+04 GAGaAcAcGTcTG
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7368 1.10e+03 CCCC.TA
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7369 5.40e+03 CAGGCG
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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 CAC3247

CAC3247 is enriched for 1 functions in 2 categories.
Enrichment Table (1)
Function System
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for CAC3247

CAC3247 has total of 42 gene neighbors in modules 151, 359
Gene neighbors (42)
Gene Common Name Description Module membership
CAC0278 CAC0278 Aspartate kinase (NCBI ptt file) 85, 151
CAC0415 CAC0415 TPR-repeat-containing protein (NCBI ptt file) 151, 217
CAC0416 CAC0416 TPR-repeat-containing protein (NCBI ptt file) 151, 217
CAC0454 CAC0454 Predicted ATP transporter permease component (NCBI ptt file) 343, 359
CAC0506 CAC0506 Penicillin-binding protein (NCBI ptt file) 151, 215
CAC0507 CAC0507 Predicted metal-dependent membrane hydrolase (NCBI ptt file) 151, 215
CAC0585 CAC0585 N-terminal CheY reciever domain fused to C-terminal uncharacterized CheX-like domain (NCBI ptt file) 66, 151
CAC0633 CAC0633 Predicted phosphatase (NCBI ptt file) 82, 151
CAC0685 CAC0685 Putative Mn transporter, NRAMP family (NCBI ptt file) 151, 215
CAC0700 cspR Predicted tRNA-methylase (SpoU class) (NCBI ptt file) 350, 359
CAC0708 CAC0708 Putative transcriptional regulator (NCBI ptt file) 20, 359
CAC0826 CAC0826 Endoglucanase family 5 (NCBI ptt file) 151, 359
CAC0849 CAC0849 Predicted transcriptional regulator (NCBI ptt file) 151, 216
CAC0961 CAC0961 Cobyric acid synthase CobQ (NCBI ptt file) 151, 201
CAC0962 CAC0962 UDP-N-acetylmuramyl tripeptide synthetase (NCBI ptt file) 79, 151
CAC1036 pykA Pyruvate kinase (NCBI ptt file) 348, 359
CAC1152 CAC1152 Hypothetical protein (NCBI ptt file) 16, 359
CAC1172 CAC1172 Predicted integrase of XerC/XerD family, diverged (NCBI ptt file) 151, 238
CAC1318 CAC1318 Hypothetical protein (NCBI ptt file) 151, 252
CAC1407 CAC1407 PTS system, beta-glucosides-specific IIABC component (NCBI ptt file) 282, 359
CAC1538 CAC1538 Predicted permease, YCXC B.subtilis ortholog (NCBI ptt file) 59, 151
CAC1559 CAC1559 Predicted transcriptional regulator (NCBI ptt file) 109, 151
CAC1660 CAC1660 Butyrate kinase, buk (NCBI ptt file) 332, 359
CAC1677 CAC1677 Predicted permease (NCBI ptt file) 259, 359
CAC1741 CAC1741 Uncharacterized conserved protein, YLBM B.subtilis ortholog (NCBI ptt file) 151, 270
CAC2056 CAC2056 Hypothetical protein (NCBI ptt file) 26, 359
CAC2140 flgG Flagellar basal body rod protein (NCBI ptt file) 192, 359
CAC2215 fliY Flagellar switch protein FliY, contains CheC-like domain (NCBI ptt file) 122, 359
CAC2255 CAC2255 Predicted permease (NCBI ptt file) 336, 359
CAC2292 CAC2292 Predicted membrane protein (NCBI ptt file) 282, 359
CAC2523 CAC2523 Glycosyltransferase (NCBI ptt file) 191, 359
CAC2655 CAC2655 Uncharacterized membrane-associated protein, DedA family (NCBI ptt file) 26, 359
CAC2732 CAC2732 ABC transporter, ATPase component (NCBI ptt file) 69, 359
CAC3225 murC UDP-N-acetylmuramate-alanine ligase (NCBI ptt file) 292, 359
CAC3247 CAC3247 Predicted transcriptional regulator, lacI/xre family (NCBI ptt file) 151, 359
CAC3263 CAC3263 Hypothetical protein (NCBI ptt file) 52, 151
CAC3272 CAC3272 Possible surface protein, responsible for cell interaction; contains cell adhesion domain and ChW-repeats (NCBI ptt file) 285, 359
CAC3352 CAC3352 Membrane associated methyl-accepting chemotaxis protein with HAMP domain (NCBI ptt file) 151, 217
CAC3384 CAC3384 Protein chain release factor B (NCBI ptt file) 343, 359
CAC3435 CAC3435 Hypothetical protein (NCBI ptt file) 185, 359
CAC3518 CAC3518 Transcriptional regulators, AcrR family (NCBI ptt file) 225, 359
CAC3675 CAC3675 Hypothetical secreted protein (NCBI ptt file) 106, 151
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 CAC3247
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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