Organism : Clostridium acetobutylicum | Module List :
CAC2232 recJ

SsDNA Exonuclease, RecJ (NCBI ptt file)

CircVis
Functional Annotations (7)
Function System
Single-stranded DNA-specific exonuclease cog/ cog
nucleic acid binding go/ molecular_function
DNA repair go/ biological_process
DNA recombination go/ biological_process
5'-3' exonuclease activity go/ molecular_function
manganese ion binding go/ molecular_function
recJ tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2232
(Mouseover regulator name to see its description)

CAC2232 is regulated by 31 influences and regulates 0 modules.
Regulators for CAC2232 recJ (31)
Regulator Module Operator
CAC0265 22 tf
CAC0310 22 tf
CAC0763 22 tf
CAC0977 22 tf
CAC1430 22 tf
CAC1832 22 tf
CAC2794 22 tf
CAC3063 22 tf
CAC3214 22 tf
CAC3360 22 tf
CAC3669 22 tf
CAC0113 315 tf
CAC0197 315 tf
CAC0382 315 tf
CAC0856 315 tf
CAC1467 315 tf
CAC1689 315 tf
CAC1696 315 tf
CAC1753 315 tf
CAC1799 315 tf
CAC2084 315 tf
CAC2143 315 tf
CAC2259 315 tf
CAC2473 315 tf
CAC2546 315 tf
CAC2773 315 tf
CAC2950 315 tf
CAC3166 315 tf
CAC3192 315 tf
CAC3418 315 tf
CAC3502 315 tf

Warning: CAC2232 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
6698 3.40e-06 TTaAGGgGGag
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6699 1.60e+03 GgAAAAGgagaAggaAaTGG
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7282 4.10e-01 gGAGttGg
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7283 7.50e+01 ctGtAGcaAg
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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 CAC2232

CAC2232 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Single-stranded DNA-specific exonuclease cog/ cog
nucleic acid binding go/ molecular_function
DNA repair go/ biological_process
DNA recombination go/ biological_process
5'-3' exonuclease activity go/ molecular_function
manganese ion binding go/ molecular_function
recJ tigr/ tigrfam
Module neighborhood information for CAC2232

CAC2232 has total of 48 gene neighbors in modules 22, 315
Gene neighbors (48)
Gene Common Name Description Module membership
CAC0176 appA Oligopeptide-binding protein, periplasmic component (NCBI ptt file) 22, 318
CAC0214 CAC0214 Endoglucanase, aminopeptidase M42 family (NCBI ptt file) 22, 320
CAC0215 CAC0215 Endoglucanase, aminopeptidase M42 family (NCBI ptt file) 22, 366
CAC0300 CAC0300 DNA-polymerase III, gamma subunit (NCBI ptt file) 315, 329
CAC0491 CAC0491 Uncharacterized probably secreted protein, homolog of YDCC B.subtilis (NCBI ptt file) 56, 315
CAC0566 CAC0566 Malate dehydrogenase (NCBI ptt file) 14, 22
CAC1026 CAC1026 Superfamily I DNA helicase (NCBI ptt file) 213, 315
CAC1243 mreC Shape-determining protein mreC (NCBI ptt file) 2, 315
CAC1290 CAC1290 Uncharacterized protein, homolog of YQFC B.subtilis (NCBI ptt file) 22, 265
CAC1291 CAC1291 Uncharacterized protein, YQFD ortholog, related spoIV gene product (NCBI ptt file) 22, 265
CAC1305 CAC1305 Uncharacterized protein similar to a protein from Cylindrotheca fusiformis plasmid (GI:99322) (NCBI ptt file) 51, 315
CAC1341 araD Ribulose-5-phosphate 4-epimerase family protein (NCBI ptt file) 22, 142
CAC1342 araA L-arabinose isomerase (NCBI ptt file) 22, 142
CAC1343 CAC1343 Transketolase (NCBI ptt file) 22, 284
CAC1403 CAC1403 Zn-dependent hydrolase, glyoxylase II family (NCBI ptt file) 100, 315
CAC1468 CAC1468 Predicted acetyltransferase (NCBI ptt file) 174, 315
CAC1630 CAC1630 Zn-dependent peptidase from MPP family (NCBI ptt file) 22, 360
CAC1684 CAC1684 TYPA/BIPA type GTPase (NCBI ptt file) 142, 315
CAC1685 CAC1685 Uncharacterized protein from YceG family (NCBI ptt file) 5, 315
CAC1686 CAC1686 S-adenosylmethionine-dependent methyltransferase (NCBI ptt file) 315, 329
CAC1687 CAC1687 Collagenase family protease (NCBI ptt file) 5, 315
CAC1689 sigK DNA-dependent RNA polymerase sigma subunit (NCBI ptt file) 39, 315
CAC1725 CAC1725 Predicted rRNA methylase, SUN family (NCBI ptt file) 159, 315
CAC1729 CAC1729 Predicted GTPase (YLOQ B.subtilis ortholog) (NCBI ptt file) 213, 315
CAC1730 CAC1730 Pentose-5-phosphate-3-epimerase, YLOR B.subtilis ortholog (NCBI ptt file) 315, 329
CAC1767 CAC1767 Hypothetical protein (NCBI ptt file) 14, 22
CAC1790 frr Ribosome recycling factor (NCBI ptt file) 310, 315
CAC1823 CAC1823 Uncharacterized conserved protein (NCBI ptt file) 51, 315
CAC1824 clpA ATP-dependent Clp proteinase (NCBI ptt file) 51, 315
CAC1829 CAC1829 Predicted inactivated Zn-dependent peptidase, PMBA ortholog (NCBI ptt file) 312, 315
CAC1954 CAC1954 Hypothetical protein (NCBI ptt file) 22, 258
CAC2232 recJ SsDNA Exonuclease, RecJ (NCBI ptt file) 22, 315
CAC2303 CAC2303 Stage V sporulation AE, SpoVAE (fragment) (NCBI ptt file) 22, 118
CAC2304 SpoVAD Stage V sporulation AD, SpoVAD (NCBI ptt file) 22, 265
CAC2673 CAC2673 NAD-dependent DNA ligase (NCBI ptt file) 35, 315
CAC2874 CAC2874 UDP-N-acetylglucosamine 2-epimerase (NCBI ptt file) 137, 315
CAC3032 CAC3032 Galactose mutarotase related enzyme (NCBI ptt file) 174, 315
CAC3274 CAC3274 Possible surface protein, responsible for cell interaction; contains cell adhesion domain and ChW-repeats (NCBI ptt file) 22, 265
CAC3275 CAC3275 Possible surface protein, responsible for cell interaction; contains cell adhesion domain and ChW-repeats (NCBI ptt file) 22, 320
CAC3304 CAC3304 Hypothetical protein, CF-42 family (NCBI ptt file) 22, 98
CAC3375 CAC3375 Alcohol dehydrogenase (NCBI ptt file) 22, 188
CAC3594 CAC3594 Glycosyltransferase (NCBI ptt file) 142, 315
CAC3678 kdpD Sensor protein KdpD (ATPase containing sensor domain and histidine kinase domain) (NCBI ptt file) 22, 78
CAC3679 kdpX Uncharacterized protein of kdp operon, kdpX (NCBI ptt file) 22, 78
CAC3680 kdpC/atkC K+-transporting ATPase, c chain (NCBI ptt file) 22, 265
CAC3681 kdpB/atkB K+-transporting ATPase, b chain (NCBI ptt file) 22, 78
CAC3682 kdpA/atkA K+-transporting ATPase, a chain (NCBI ptt file) 22, 265
CAC3684 CAC3684 Polygalacturonase (NCBI ptt file) 22, 118
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 CAC2232
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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