Organism : Clostridium acetobutylicum | Module List :
CAC1310

Integrase XerD family protein (similarity only with C-term. part (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
DNA binding go/ molecular_function
DNA recombination go/ biological_process
DNA integration go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1310
(Mouseover regulator name to see its description)

CAC1310 is regulated by 23 influences and regulates 0 modules.
Regulators for CAC1310 (23)
Regulator Module Operator
CAC0723 205 tf
CAC1463 205 tf
CAC1483 205 tf
CAC2055 205 tf
CAC2113 205 tf
CAC2236 205 tf
CAC3406 205 tf
CAC3433 205 tf
CAC3466 205 tf
CAC3487 205 tf
CAC3651 205 tf
CAC0445 141 tf
CAC0951 141 tf
CAC1463 141 tf
CAC1668 141 tf
CAC1770 141 tf
CAC1915 141 tf
CAC2236 141 tf
CAC2768 141 tf
CAC3199 141 tf
CAC3429 141 tf
CAC3472 141 tf
CAC3507 141 tf

Warning: CAC1310 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
6934 1.10e-03 GGaGgagt
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6935 7.30e+03 AGcCCG
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7062 6.90e+02 cGcaTTcCAAAAGcatCAAcCCCC
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7063 2.30e+03 tTGgAgAagTaattGgtttagAGT
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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 CAC1310

CAC1310 is enriched for 3 functions in 2 categories.
Enrichment Table (3)
Function System
DNA binding go/ molecular_function
DNA recombination go/ biological_process
DNA integration go/ biological_process
Module neighborhood information for CAC1310

CAC1310 has total of 41 gene neighbors in modules 141, 205
Gene neighbors (41)
Gene Common Name Description Module membership
CAC0136 CAC0136 Hypothetical protein (NCBI ptt file) 69, 205
CAC0137 CAC0137 Hypothetical protein, CF-5 family (NCBI ptt file) 69, 205
CAC0226 CAC0226 ABC transporter, ATP-binding protein (NCBI ptt file) 141, 145
CAC0260 nifV Homocitrate syntase, omega subunit nifV (nivO) (NCBI ptt file) 141, 169
CAC0364 CAC0364 Metal-dependent hydrolases of the metallobeta-lactamase superfamily (NCBI ptt file) 141, 333
CAC0538 CAC0538 Beta-mannanase ManB-like enzyme, contains ChW-repeats (NCBI ptt file) 4, 205
CAC0621 CAC0621 Exopolyphosphatase (NCBI ptt file) 205, 336
CAC0656 CAC0656 Predicted transposase (3' fragment) (NCBI ptt file) 205, 267
CAC0657 CAC0657 Predicted transposase (5' fragment) (NCBI ptt file) 205, 267
CAC0774 CAC0774 Uncharacterized conserved protein (NCBI ptt file) 157, 205
CAC0922 CAC0922 Uncharacterized small conserved protein, homolog of yfjA/yukE B.subtilis (NCBI ptt file) 141, 145
CAC1310 CAC1310 Integrase XerD family protein (similarity only with C-term. part (NCBI ptt file) 141, 205
CAC1447 CAC1447 MDR-type permease, probably tetracycline resistance protein (NCBI ptt file) 141, 307
CAC1507 phoR Sensory transduction histidine kinase (with HAMP domain) (NCBI ptt file) 205, 346
CAC1703 CAC1703 Methyl-accepting chemotaxis protein (fragment) (NCBI ptt file) 205, 336
CAC1963 CAC1963 5'-nucleotidase/2',3'-cyclic phosphodiesterase related enzyme (NCBI ptt file) 69, 205
CAC1976 CAC1976 Hypothetical secreted protein (NCBI ptt file) 205, 336
CAC1977 CAC1977 Predicted membrane protein (NCBI ptt file) 205, 336
CAC1978 CAC1978 Predicted membrane protein (NCBI ptt file) 205, 336
CAC1980 CAC1980 Predicted ATPase involved in pili biogenesis (NCBI ptt file) 205, 336
CAC2028 CAC2028 Hypothetical protein, CF-4 family (NCBI ptt file) 205, 208
CAC2029 CAC2029 Hypothetical protein (NCBI ptt file) 141, 333
CAC2044 CAC2044 Hypothetical protein (NCBI ptt file) 141, 333
CAC2179 CAC2179 Nucleoside-diphosphate-sugar epimerase (NCBI ptt file) 141, 145
CAC2419 CAC2419 Methyl-accepting chemotaxis protein (NCBI ptt file) 69, 205
CAC2493 CAC2493 Phospholipase C family protein (NCBI ptt file) 205, 208
CAC2567 CAC2567 Superoxide dismutase (Fe/Mn family) (NCBI ptt file) 141, 190
CAC2614 CAC2614 Beta-phosphoglucomutase (NCBI ptt file) 141, 190
CAC2821 CAC2821 Methyl-accepting chemotaxis protein (NCBI ptt file) 141, 145
CAC2911 CAC2911 Glycosyltransferase (NCBI ptt file) 141, 145
CAC3276 nrdB Ribonucleotide reductase beta subunit (NCBI ptt file) 141, 241
CAC3385 CAC3385 Hypothetical protein (NCBI ptt file) 69, 205
CAC3389 CAC3389 Possible S-layer protein (NCBI ptt file) 141, 145
CAC3431 CAC3431 Membrane export protein, related to SecD/SecF protein exporters (NCBI ptt file) 141, 333
CAC3432 CAC3432 Alpha/beta superfamily hydrolase (NCBI ptt file) 141, 333
CAC3434 CAC3434 Hypothetical protein (NCBI ptt file) 205, 344
CAC3480 CAC3480 Hypothetical protein (NCBI ptt file) 141, 190
CAC3490 CAC3490 DNA gyrase inhibitory protein, GyrI (NCBI ptt file) 205, 301
CAC3492 CAC3492 Uncharacterized conserved protein (NCBI ptt file) 205, 217
CAC3565 CAC3565 Uncharacterized secreted protein, containing cell adhesion domain (NCBI ptt file) 205, 267
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 CAC1310
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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