Organism : Clostridium acetobutylicum | Module List :
CAC3716 lonB

Lon-like ATP-dependent protease (NCBI ptt file)

CircVis
Functional Annotations (14)
Function System
Predicted ATP-dependent protease cog/ cog
ATP-dependent peptidase activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
DNA repair go/ biological_process
DNA recombination go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
proteolysis go/ biological_process
transcription factor binding go/ molecular_function
endopeptidase La activity go/ molecular_function
four-way junction helicase activity go/ molecular_function
ATPase activity go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
spore_lon_C tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3716
(Mouseover regulator name to see its description)

CAC3716 is regulated by 24 influences and regulates 0 modules.
Regulators for CAC3716 lonB (24)
Regulator Module Operator
CAC0422 114 tf
CAC0550 114 tf
CAC0863 114 tf
CAC1404 114 tf
CAC1469 114 tf
CAC2430 114 tf
CAC2794 114 tf
CAC3475 114 tf
CAC3487 114 tf
CAC3606 114 tf
CAC0144 36 tf
CAC0255 36 tf
CAC0299 36 tf
CAC0763 36 tf
CAC0863 36 tf
CAC1046 36 tf
CAC1682 36 tf
CAC1719 36 tf
CAC1799 36 tf
CAC2084 36 tf
CAC2430 36 tf
CAC3267 36 tf
CAC3345 36 tf
CAC3646 36 tf

Warning: CAC3716 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
6726 4.80e-10 Atat.AGgaGGaga
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6727 8.40e+03 GAGGTcG
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6880 7.50e+01 aaGAGggataA
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6881 3.20e+02 CCActcaAcC
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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 CAC3716

CAC3716 is enriched for 14 functions in 3 categories.
Enrichment Table (14)
Function System
Predicted ATP-dependent protease cog/ cog
ATP-dependent peptidase activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
DNA repair go/ biological_process
DNA recombination go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
proteolysis go/ biological_process
transcription factor binding go/ molecular_function
endopeptidase La activity go/ molecular_function
four-way junction helicase activity go/ molecular_function
ATPase activity go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
spore_lon_C tigr/ tigrfam
Module neighborhood information for CAC3716

CAC3716 has total of 46 gene neighbors in modules 36, 114
Gene neighbors (46)
Gene Common Name Description Module membership
CAC0138 CAC0138 ABC transporter, ATP-binding component (NCBI ptt file) 36, 114
CAC0139 CAC0139 Predicted permease (NCBI ptt file) 36, 114
CAC0140 CAC0140 Predicted permease (NCBI ptt file) 67, 114
CAC0141 CAC0141 Membrane permease, predicted cation efflux pumps (NCBI ptt file) 36, 114
CAC0158 glmS Glucoseamine-fructose-6-phosphate aminotransferase (gene glmS) (NCBI ptt file) 36, 84
CAC0301 CAC0301 Signal peptidase II (PSP1) homolog, YAAT B.subtilis ortholog (NCBI ptt file) 36, 271
CAC0970 CAC0970 Isopropylmalate synthase (NCBI ptt file) 114, 127
CAC0971 citB Aconitase A (NCBI ptt file) 114, 127
CAC0972 citC Isocitrate dehydrogenase (NCBI ptt file) 114, 127
CAC1336 CAC1336 Hypothetical protein (NCBI ptt file) 114, 127
CAC1337 CAC1337 Spore coat protein COTJB (NCBI ptt file) 114, 127
CAC1338 CAC1338 Spore coat protein COTJC (NCBI ptt file) 114, 127
CAC1469 CAC1469 Iron-dependent transcription repressor (NCBI ptt file) 114, 127
CAC1572 CAC1572 Fructose-1,6-bisphosphatase (YYDE B.subtils ortholog) (NCBI ptt file) 100, 114
CAC1629 CAC1629 Putative intracellular protease/amidase, ThiJ family (NCBI ptt file) 36, 45
CAC1633 CAC1633 Protein from bacterioferritin family (NCBI ptt file) 114, 127
CAC1656 CAC1656 Hypothetical protein, CF-39 family (NCBI ptt file) 114, 273
CAC1734 CAC1734 Uncharacterized, alkaline shock induced protein (NCBI ptt file) 36, 329
CAC1735 CAC1735 Predicted kinase related to hydroxyacetone kinase, YLOV ortholog (NCBI ptt file) 36, 335
CAC1836 mutL DNA mismatch repair enzyme, MutL (NCBI ptt file) 36, 159
CAC1838 CAC1838 Predicted Fe-S oxidoreductase, YMCB B.subtilis ortholog (NCBI ptt file) 36, 159
CAC1866 CAC1866 Putative 4-Cys ferredoxin (NCBI ptt file) 114, 127
CAC2243 asnB N-terminal domain of asparagine synthase (NCBI ptt file) 100, 114
CAC2249 CAC2249 C-terminal domain of asparagine synthase (NCBI ptt file) 114, 300
CAC2565 CAC2565 NifU-related domain containing protein (NCBI ptt file) 36, 153
CAC2629 CAC2629 Hypothetical secreted protein (NCBI ptt file) 36, 310
CAC2747 CAC2747 Protein containing LysM repeats (N-terminal domain) and domain related to chitinase (NCBI ptt file) 114, 127
CAC2797 CAC2797 Hypothetical protein (NCBI ptt file) 114, 127
CAC2858 mreV Shape-determining protein envB (HSP70 family charepones) (NCBI ptt file) 36, 63
CAC2880 CAC2880 Ribose 5-phosphate isomerase, RpiB (NCBI ptt file) 36, 329
CAC2909 CAC2909 Spore coat protein cotS related (diverged) (NCBI ptt file) 114, 190
CAC2968 CAC2968 Mannose-1-phosphate guanylyltransferase (NCBI ptt file) 114, 127
CAC3017 CAC3017 Predicted xylanase/chitin deacetylase (NCBI ptt file) 36, 335
CAC3018 CAC3018 Rubrerythrin (NCBI ptt file) 114, 127
CAC3040 CAC3040 CPSC/CAPB subfamily ATPase (NCBI ptt file) 36, 235
CAC3078 CAC3078 Uncharacterized secreted protein, YBBR Bacillus subtilis homolog (NCBI ptt file) 114, 142
CAC3138 fus Translation elongation factor EF-G (NCBI ptt file) 36, 335
CAC3187 CAC3187 Predicted nucleic-acid-binding protein protein, containing HHH domain, YACK B.subtilis ortholog (NCBI ptt file) 36, 329
CAC3188 sms Predicted ATP-dependent serine protease, RADA homolog (NCBI ptt file) 36, 271
CAC3674 CAC3674 Two CBS domain containing protein (NCBI ptt file) 114, 300
CAC3708 CAC3708 Hypothetical protein (NCBI ptt file) 36, 44
CAC3709 CAC3709 DNA segregation ATPase, FtsK/SpoIIIE family, YUKA B.subtilis ortholog (NCBI ptt file) 36, 44
CAC3710 CAC3710 Uncharacterized protein, YUKC B.subtilis homolog (NCBI ptt file) 36, 44
CAC3711 CAC3711 Hypothetical protein (NCBI ptt file) 36, 44
CAC3716 lonB Lon-like ATP-dependent protease (NCBI ptt file) 36, 114
CAC3717 rplI Ribosomal protein L9 (NCBI ptt file) 114, 243
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 CAC3716
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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