Organism : Clostridium acetobutylicum | Module List :
CAC2639 clpX

ATP-dependent protease Clp, ATPase subunit ClpX (NCBI ptt file)

CircVis
Functional Annotations (12)
Function System
ATP-dependent protease Clp, ATPase subunit cog/ cog
ATP binding go/ molecular_function
DNA repair go/ biological_process
DNA recombination go/ biological_process
zinc ion binding go/ molecular_function
endopeptidase Clp activity go/ molecular_function
four-way junction helicase activity go/ molecular_function
protein transport go/ biological_process
ATPase activity go/ molecular_function
protein metabolic process go/ biological_process
protein dimerization activity go/ molecular_function
clpX tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2639
(Mouseover regulator name to see its description)

CAC2639 is regulated by 16 influences and regulates 0 modules.
Regulators for CAC2639 clpX (16)
Regulator Module Operator
CAC0299 128 tf
CAC1280 128 tf
CAC1682 128 tf
CAC2071 128 tf
CAC0191 233 tf
CAC0254 233 tf
CAC0445 233 tf
CAC0807 233 tf
CAC0977 233 tf
CAC1682 233 tf
CAC1832 233 tf
CAC1941 233 tf
CAC2084 233 tf
CAC2546 233 tf
CAC3224 233 tf
CAC3731 233 tf

Warning: CAC2639 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
6908 1.40e-08 A.CaCCtCttT
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6909 1.20e+04 CCTGAC
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7118 4.30e+01 GagaGgaA
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7119 2.20e+04 GCAAAacGG
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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 CAC2639

CAC2639 is enriched for 12 functions in 3 categories.
Enrichment Table (12)
Function System
ATP-dependent protease Clp, ATPase subunit cog/ cog
ATP binding go/ molecular_function
DNA repair go/ biological_process
DNA recombination go/ biological_process
zinc ion binding go/ molecular_function
endopeptidase Clp activity go/ molecular_function
four-way junction helicase activity go/ molecular_function
protein transport go/ biological_process
ATPase activity go/ molecular_function
protein metabolic process go/ biological_process
protein dimerization activity go/ molecular_function
clpX tigr/ tigrfam
Module neighborhood information for CAC2639

CAC2639 has total of 36 gene neighbors in modules 128, 233
Gene neighbors (36)
Gene Common Name Description Module membership
CAC0091 ilvC Ketol-acid reductoisomerase (NCBI ptt file) 128, 334
CAC0499 CAC0499 Carboxyl-terminal protease (NCBI ptt file) 182, 233
CAC0711 tpi Triosephosphate isomerase (NCBI ptt file) 128, 292
CAC0713 eno Enolase (NCBI ptt file) 128, 363
CAC0807 CAC0807 Cold shock protein (NCBI ptt file) 231, 233
CAC0901 CAC0901 Probably O-sialoglycoprotein endopeptidase (NCBI ptt file) 160, 233
CAC0950 CAC0950 Predicted membrane protein (NCBI ptt file) 152, 233
CAC0967 CAC0967 Probably membrane protein (NCBI ptt file) 162, 233
CAC1280 hrcA Transcriptional regulator of heat shock genes, HrcA (NCBI ptt file) 128, 201
CAC1281 grpE Molecular chaperone GrpE (NCBI ptt file) 128, 221
CAC1283 dnaJ Molecular chaperones DnaJ (HSP40 family) (NCBI ptt file) 128, 221
CAC1287 CAC1287 HIT family hydrolase (NCBI ptt file) 128, 289
CAC1288 rpsU Ribosomal protein S21 (NCBI ptt file) 128, 231
CAC1679 CAC1679 Hypothetical protein (NCBI ptt file) 64, 128
CAC1682 CAC1682 Ferric uptake regulation protein (NCBI ptt file) 128, 289
CAC1693 ftsZ Cell division GTPase FtsZ (NCBI ptt file) 20, 233
CAC1808 pnpA Polyribonucleotide nucleotidyltransferase (NCBI ptt file) 229, 233
CAC1815 recA RECA recombinase, ATPase (NCBI ptt file) 92, 233
CAC1816 CAC1816 HD superfamily hydrolase, YMDA B.subtilis ortholog (NCBI ptt file) 128, 233
CAC1958 CAC1958 Predicted aldo/keto reductase, YTBE/YVGN B.subtilis ortholog (NCBI ptt file) 128, 289
CAC2071 CAC2071 Spo0A protein, (CheY-like receiver domain and HTH-type DNA binding domain) (NCBI ptt file) 128, 289
CAC2110 CAC2110 GAF domain-containing protein (NCBI ptt file) 233, 304
CAC2119 CAC2119 Predicted integral membrane protein, YggT family (NCBI ptt file) 128, 295
CAC2123 sbp Small basic protein, sbp, uncharacterized (NCBI ptt file) 67, 128
CAC2124 CAC2124 Conserved membrane protein (NCBI ptt file) 67, 128
CAC2334 CAC2334 UDP-glucose 4-epimerase (NCBI ptt file) 128, 289
CAC2335 CAC2335 UTP-glucose-1-phosphate uridylyltransferase (NCBI ptt file) 128, 289
CAC2622 comE ComE-like protein, Metallo beta-lactamase superfamily hydrolase (NCBI ptt file) 152, 233
CAC2639 clpX ATP-dependent protease Clp, ATPase subunit ClpX (NCBI ptt file) 128, 233
CAC2640 clpP Protease subunits of ATP-dependent protease, ClpP (NCBI ptt file) 128, 289
CAC2777 CAC2777 Glutaredoxin (NCBI ptt file) 49, 233
CAC2787 CAC2787 Serine/threonine protein phosphatase (NCBI ptt file) 109, 128
CAC2847 CAC2847 Ribosome-associated protein Y (PSrp-1) (NCBI ptt file) 128, 201
CAC2904 CAC2904 Uncharacterized protein, VEG B.subtilis ortholog (NCBI ptt file) 233, 298
CAC3033 CAC3033 Uncharacterized protein containing conserved domain, related to YABE B.subtilis C-terminal domain (NCBI ptt file) 86, 233
CAC3383 CAC3383 Uncharacterized conserved protein, RtcB/UPF0027 family (NCBI ptt file) 72, 233
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 CAC2639
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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