Organism : Clostridium acetobutylicum | Module List :
CAC1463

Predicted transcriptional regulator (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1463
(Mouseover regulator name to see its description)

CAC1463 is regulated by 14 influences and regulates 18 modules.
Regulators for CAC1463 (14)
Regulator Module Operator
CAC0144 342 tf
CAC0155 342 tf
CAC0183 342 tf
CAC0807 342 tf
CAC0977 342 tf
CAC1430 342 tf
CAC1463 342 tf
CAC1867 342 tf
CAC2955 342 tf
CAC2966 342 tf
CAC0189 145 tf
CAC1463 145 tf
CAC3429 145 tf
CAC3472 145 tf

Warning: CAC1463 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
6942 8.80e+00 AaaGgAaGggg
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6943 7.60e+03 GGCtGC
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7336 1.20e+02 aGGa..tG
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7337 1.60e+03 gg.A.cAgtAGtAgg
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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 CAC1463

CAC1463 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for CAC1463

CAC1463 has total of 39 gene neighbors in modules 145, 342
Gene neighbors (39)
Gene Common Name Description Module membership
CAC0154 MtlA PTS system, mannitol-specific IIBC component (gene MtlA) (NCBI ptt file) 301, 342
CAC0155 MtlR Putative regulator of the PTS system for mannitol (gene MltR) (NCBI ptt file) 170, 342
CAC0156 MltF PTS system, mannitol-specific IIA domain (Ntr-type) (gene MltF) (NCBI ptt file) 170, 342
CAC0157 MtlD Possible sigma factor, diverged member of sigF/sigE/sigG family (NCBI ptt file) 170, 342
CAC0221 CAC0221 Aspartate aminotransferase (NCBI ptt file) 342, 343
CAC0226 CAC0226 ABC transporter, ATP-binding protein (NCBI ptt file) 141, 145
CAC0319 CAC0319 ABC transporter ATP-binding protein (NCBI ptt file) 6, 342
CAC0320 CAC0320 Predicted permease (NCBI ptt file) 338, 342
CAC0428 CAC0428 Sugar permease (NCBI ptt file) 108, 145
CAC0598 gerKC Spore germination protein, gerKC (NCBI ptt file) 24, 145
CAC0622 CAC0622 Polyphosphate kinase (NCBI ptt file) 125, 145
CAC0750 CAC0750 Hypothetical protein (NCBI ptt file) 62, 342
CAC0795 CAC0795 Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file) 288, 342
CAC0828 CAC0828 Hypothetical protein (NCBI ptt file) 145, 202
CAC0922 CAC0922 Uncharacterized small conserved protein, homolog of yfjA/yukE B.subtilis (NCBI ptt file) 141, 145
CAC0924 CAC0924 Predicted membrane protein (NCBI ptt file) 145, 190
CAC1141 CAC1141 Hypothetical protein (NCBI ptt file) 16, 342
CAC1321 glpK Glycerol kinase, GLPK (NCBI ptt file) 272, 342
CAC1420 CAC1420 Protein with a fusion of two uncharacterized domains, typical for archaea (NCBI ptt file) 145, 361
CAC1463 CAC1463 Predicted transcriptional regulator (NCBI ptt file) 145, 342
CAC1646 CAC1646 Hypothetical protein, CF-7 family (NCBI ptt file) 148, 342
CAC1867 CAC1867 Transcriptional regulator (phage-related) (Xre family) (NCBI ptt file) 301, 342
CAC1870 CAC1870 Hypothetical protein (NCBI ptt file) 44, 342
CAC1871 CAC1871 FtsK-like DNA segregation ATPase, YDCQ B.subtilis ortholog (NCBI ptt file) 332, 342
CAC1872 repB Replication initiation protein REP (NCBI ptt file) 54, 342
CAC1901 CAC1901 Hypothetical protein (NCBI ptt file) 54, 342
CAC1942 CAC1942 Hypothetical protein (NCBI ptt file) 54, 342
CAC2179 CAC2179 Nucleoside-diphosphate-sugar epimerase (NCBI ptt file) 141, 145
CAC2547 CAC2547 Possible membrane-associated methyl-accepting chemotaxis protein fused to HAMP domain (NCBI ptt file) 145, 258
CAC2821 CAC2821 Methyl-accepting chemotaxis protein (NCBI ptt file) 141, 145
CAC2911 CAC2911 Glycosyltransferase (NCBI ptt file) 141, 145
CAC2955 lacR Lactose phosphotransferase system repressor lacR (NCBI ptt file) 288, 342
CAC2964 lacE PTS system lactose-specific enzyme IIBC (NCBI ptt file) 288, 342
CAC3243 CAC3243 Membrane associated methyl-accepting chemotaxis protein (NCBI ptt file) 113, 342
CAC3246 CAC3246 Hypothetical protein (NCBI ptt file) 145, 190
CAC3270 CAC3270 Permease, predicted cation efflux pump (NCBI ptt file) 108, 145
CAC3372 CAC3372 Uncharacterized conserved membrane protein, YCAP family (NCBI ptt file) 145, 361
CAC3389 CAC3389 Possible S-layer protein (NCBI ptt file) 141, 145
CAC3608 CAC3608 ABC-type MDR transport system, ATPase component (NCBI ptt file) 141, 145
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 CAC1463
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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