Organism : Clostridium acetobutylicum | Module List :
CAC1009

Cell wall biogenesis enzyme (N-terminal domain related to N-Acetylmuramoyl-L-alanine amidase and C-terminal domain related to L-alanoyl-D-glutamate peptidase); peptodoglycan-binding domain (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Putative peptidoglycan-binding domain-containing protein cog/ cog
proteolysis go/ biological_process
peptidase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1009
(Mouseover regulator name to see its description)

CAC1009 is regulated by 20 influences and regulates 0 modules.
Regulators for CAC1009 (20)
Regulator Module Operator
CAC0144 267 tf
CAC0514 267 tf
CAC1843 267 tf
CAC3424 267 tf
CAC3606 267 tf
CAC3649 267 tf
CAC3695 267 tf
CAC0023 155 tf
CAC0078 155 tf
CAC0289 155 tf
CAC0856 155 tf
CAC1264 155 tf
CAC1467 155 tf
CAC1481 155 tf
CAC1719 155 tf
CAC2084 155 tf
CAC2306 155 tf
CAC3271 155 tf
CAC3409 155 tf
CAC3424 155 tf

Warning: CAC1009 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
6962 1.20e+01 tgGAGGT
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6963 4.70e+04 CccCccTTG
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7186 4.50e-11 aGGaGG
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7187 1.80e+03 cTTctTCGc
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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 CAC1009

CAC1009 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Putative peptidoglycan-binding domain-containing protein cog/ cog
proteolysis go/ biological_process
peptidase activity go/ molecular_function
Module neighborhood information for CAC1009

CAC1009 has total of 37 gene neighbors in modules 155, 267
Gene neighbors (37)
Gene Common Name Description Module membership
CAC0190 CAC0190 Beta-lactamase (NCBI ptt file) 60, 155
CAC0656 CAC0656 Predicted transposase (3' fragment) (NCBI ptt file) 205, 267
CAC0657 CAC0657 Predicted transposase (5' fragment) (NCBI ptt file) 205, 267
CAC0735 CAC0735 Transmembrane protein, ortholog TM1408 (NCBI ptt file) 231, 267
CAC0800 ubiA 4-hydroxybenzoate octaprenyltranferase related protein (NCBI ptt file) 183, 267
CAC0881 CAC0881 Hypothetical protein (NCBI ptt file) 267, 344
CAC1003 CAC1003 Superfamily I DNA helicase (rep-like helicase) (NCBI ptt file) 267, 317
CAC1009 CAC1009 Cell wall biogenesis enzyme (N-terminal domain related to N-Acetylmuramoyl-L-alanine amidase and C-terminal domain related to L-alanoyl-D-glutamate peptidase); peptodoglycan-binding domain (NCBI ptt file) 155, 267
CAC1010 CAC1010 Predicted phosphohydrolase, Icc family (NCBI ptt file) 155, 178
CAC1068 CAC1068 Hypothetical protein, CF-25 family (NCBI ptt file) 176, 267
CAC1078 CAC1078 Predicted phosphohydrolase, Icc family (NCBI ptt file) 53, 267
CAC1170 xerD Integrase/recombinase (xerD/xerC family) (NCBI ptt file) 53, 267
CAC1351 CAC1351 Periplasmic sugar-binding protein (NCBI ptt file) 24, 267
CAC1472 CAC1472 Amino acid permease (NCBI ptt file) 40, 267
CAC1664 glgP Glycogen phosphorylase (NCBI ptt file) 18, 155
CAC1768 CAC1768 Uncharacterized conserved protein, TraB family (NCBI ptt file) 60, 155
CAC1775 CAC1775 Predicted membrane protein (NCBI ptt file) 18, 155
CAC1856 CAC1856 Ribonuclease HI (NCBI ptt file) 238, 267
CAC2042 CAC2042 ABC transported MDR-type, permease component (NCBI ptt file) 60, 155
CAC2098 CAC2098 Hypothetical protein (NCBI ptt file) 267, 312
CAC2289 CAC2289 Biotin carboxyl carrier protein (NCBI ptt file) 60, 155
CAC2393 CAC2393 Uncharacterized ABC transporter, ATPase component (NCBI ptt file) 231, 267
CAC2407 CAC2407 CheY-like receiver domain of response regulator (NCBI ptt file) 7, 155
CAC2408 CAC2408 Glycosyltransferase (NCBI ptt file) 7, 155
CAC2467 CAC2467 Hypothetical protein (NCBI ptt file) 110, 267
CAC2508 CAC2508 Nitroreductase family protein (NCBI ptt file) 29, 267
CAC2514 CAC2514 Beta galactosidase (NCBI ptt file) 60, 155
CAC2580 CAC2580 Hypothetical protein, CF-41 family (NCBI ptt file) 155, 293
CAC2597 CAC2597 Hypothetical protein (NCBI ptt file) 60, 267
CAC2599 CAC2599 Hypothetical protein (NCBI ptt file) 110, 267
CAC2663 CAC2663 Protein containing cell-wall hydrolase domain (NCBI ptt file) 130, 155
CAC2679 CAC2679 Pullulanase (NCBI ptt file) 267, 279
CAC2944 CAC2944 N-terminal domain intergin-like repeats and c-terminal- cell wall-associated hydrolase domain (NCBI ptt file) 155, 293
CAC2988 CAC2988 Uncharacterized conserved protein, YABE B.subtilis ortholog (NCBI ptt file) 267, 345
CAC3411 CAC3411 Homolog of plant auxin-responsive GH3-like protein (NCBI ptt file) 60, 155
CAC3565 CAC3565 Uncharacterized secreted protein, containing cell adhesion domain (NCBI ptt file) 205, 267
CAC3612 CAC3612 Hypothetical protein (NCBI ptt file) 18, 155
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 CAC1009
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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