Organism : Clostridium acetobutylicum | Module List :
CAC1698

Uncharacterized conserved protein, YTCG B.subtilis ortholog (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains cog/ cog
TIGR00244 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1698
(Mouseover regulator name to see its description)

CAC1698 is regulated by 21 influences and regulates 17 modules.
Regulators for CAC1698 (21)
Regulator Module Operator
CAC0144 130 tf
CAC0155 130 tf
CAC0265 130 tf
CAC0977 130 tf
CAC1333 130 tf
CAC1569 130 tf
CAC1698 130 tf
CAC2394 130 tf
CAC2476 130 tf
CAC3647 130 tf
CAC0162 152 tf
CAC0183 152 tf
CAC0459 152 tf
CAC0465 152 tf
CAC0977 152 tf
CAC1675 152 tf
CAC1698 152 tf
CAC2236 152 tf
CAC2546 152 tf
CAC3037 152 tf
CAC3647 152 tf

Warning: CAC1698 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
6912 1.60e-05 .CTcCC
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6913 1.10e+00 AAgtAaatgttTaagAgtTaG
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6956 2.40e-02 tTtC.CC.ttc
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6957 2.40e+04 GCTCAC
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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 CAC1698

CAC1698 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains cog/ cog
TIGR00244 tigr/ tigrfam
Module neighborhood information for CAC1698

CAC1698 has total of 36 gene neighbors in modules 130, 152
Gene neighbors (36)
Gene Common Name Description Module membership
CAC0008 CAC0008 Predicted HD superfamily hydrolase (NCBI ptt file) 8, 130
CAC0028 hydA Hydrogene dehydrogenase (NCBI ptt file) 8, 130
CAC0083 CAC0083 PemK family of DNA-binding proteins (NCBI ptt file) 152, 260
CAC0459 CAC0459 NtrC family transcriptional regulator (PAS and AAA domains) (NCBI ptt file) 92, 152
CAC0500 CAC0500 Membrane protein containing C-terminal PDZ domain (NCBI ptt file) 152, 182
CAC0775 CAC0775 ATP-utilizing enzyme of the PP-loop superfamily (NCBI ptt file) 8, 130
CAC0950 CAC0950 Predicted membrane protein (NCBI ptt file) 152, 233
CAC0969 CAC0969 Hypothetical protein (NCBI ptt file) 152, 182
CAC0977 asnC Transcriptional regulator, Lrp family (NCBI ptt file) 152, 268
CAC1121 CAC1121 Predicted membrane protein (NCBI ptt file) 134, 152
CAC1214 CAC1214 Xre family DNA-binding domain and TPR-repeat containing protein (NCBI ptt file) 152, 268
CAC1698 CAC1698 Uncharacterized conserved protein, YTCG B.subtilis ortholog (NCBI ptt file) 130, 152
CAC1778 CAC1778 Amidase from nicotinamidase family (NCBI ptt file) 130, 303
CAC1868 CAC1868 Uncharacterized secreted protein, homolog YXKC Bacillus subtilis (NCBI ptt file) 152, 348
CAC2069 CAC2069 Hypothetical protein (NCBI ptt file) 152, 176
CAC2094 efp Translation elongation factor P (NCBI ptt file) 152, 281
CAC2107 CAC2107 Contains cell adhesion domain (NCBI ptt file) 130, 198
CAC2245 CAC2245 Stress-induced protein OsmC (NCBI ptt file) 40, 130
CAC2275 apt Adenine phosphoribosyltransferase; Apt (NCBI ptt file) 152, 276
CAC2295 CAC2295 Uncharacterized conserved protein, YebC family (NCBI ptt file) 152, 296
CAC2312 CAC2312 Rhamnosyl transferase, rfbQ (NCBI ptt file) 8, 130
CAC2313 CAC2313 Glycosyltransferase (NCBI ptt file) 8, 130
CAC2314 CAC2314 Membrane protein involved in the export of O-antigen and teichoic acid, RfbX family (NCBI ptt file) 8, 130
CAC2366 CAC2366 Predicted membrane protein (NCBI ptt file) 85, 152
CAC2395 CAC2395 Predicted phosphatase, YWOA B.subtilis ortholog (NCBI ptt file) 40, 130
CAC2417 CAC2417 Hypothetical protein (NCBI ptt file) 152, 162
CAC2487 CAC2487 Predicted acetyltransferase (NCBI ptt file) 130, 162
CAC2500 CAC2500 Uncharacterized conserved membrane protein, YgiH/UPF0078 family (NCBI ptt file) 130, 162
CAC2501 CAC2501 Membrane protein, predicted transporter of cations and cationic drugs (NCBI ptt file) 130, 198
CAC2502 CAC2502 Predicted permease (NCBI ptt file) 130, 341
CAC2622 comE ComE-like protein, Metallo beta-lactamase superfamily hydrolase (NCBI ptt file) 152, 233
CAC2663 CAC2663 Protein containing cell-wall hydrolase domain (NCBI ptt file) 130, 155
CAC2819 murE UDP-N-acetylmuramyl tripeptide synthase, MURE (NCBI ptt file) 130, 252
CAC2967 CAC2967 Alpha-acetolactate decarboxylase (NCBI ptt file) 152, 206
CAC3193 CAC3193 Hypothetical protein (NCBI ptt file) 130, 149
CAC3528 CAC3528 Hypothetical protein (NCBI ptt file) 130, 162
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 CAC1698
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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