Organism : Clostridium acetobutylicum | Module List :
CAC1766

Predicted sigma factor (NCBI ptt file)

CircVis
Functional Annotations (10)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sigma70-ECF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1766
(Mouseover regulator name to see its description)

CAC1766 is regulated by 22 influences and regulates 42 modules.
Regulators for CAC1766 (22)
Regulator Module Operator
CAC0078 200 tf
CAC0183 200 tf
CAC0191 200 tf
CAC0284 200 tf
CAC0550 200 tf
CAC0681 200 tf
CAC0723 200 tf
CAC0849 200 tf
CAC1766 200 tf
CAC2052 200 tf
CAC2113 200 tf
CAC3731 200 tf
CAC0183 236 tf
CAC0191 236 tf
CAC1463 236 tf
CAC1467 236 tf
CAC1668 236 tf
CAC1753 236 tf
CAC2471 236 tf
CAC3037 236 tf
CAC3507 236 tf
CAC3651 236 tf

Warning: CAC1766 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
7052 5.90e+02 AGgggGGattaA
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7053 2.20e+04 ctCACACAC
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7124 2.20e+02 gGAGGT
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7125 1.10e+03 AAggGtGGAT
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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 CAC1766

CAC1766 is enriched for 10 functions in 3 categories.
Module neighborhood information for CAC1766

CAC1766 has total of 35 gene neighbors in modules 200, 236
Gene neighbors (35)
Gene Common Name Description Module membership
CAC0035 CAC0035 Serine/threonine phosphatase (inactivated protein) (NCBI ptt file) 236, 353
CAC0182 CAC0182 Beta-glucosidase homolog (NCBI ptt file) 236, 320
CAC0184 CAC0184 Predicted acetyltransferase (NCBI ptt file) 236, 314
CAC0191 CAC0191 Transcriptional regulator, RpiR family (NCBI ptt file) 200, 236
CAC0430 CAC0430 Glycerophosphoryl diester phosphodiesterase (NCBI ptt file) 165, 236
CAC0582 CAC0582 Cobyrinic acid a,c-diamide synthase CobB/CbiA (CBIB protein) (NCBI ptt file) 236, 288
CAC0786 CAC0786 Uncharacterized conserved protein, repeats (NCBI ptt file) 154, 236
CAC0799 psd Phosphatidylserine decarboxylase (NCBI ptt file) 183, 236
CAC1035 CAC1035 Hypothetical protein (NCBI ptt file) 200, 334
CAC1054 CAC1054 Arginase (NCBI ptt file) 165, 236
CAC1246 pbpA Penicillin-binding protein 2 (NCBI ptt file) 56, 200
CAC1466 CAC1466 Hypothetical protein (NCBI ptt file) 39, 236
CAC1541 CAC1541 Hypothetical protein, CF-36 family (NCBI ptt file) 200, 265
CAC1545 deoC Deoxyribose-phosphate aldolase (NCBI ptt file) 172, 200
CAC1546 deoA Pyrimidine-nucleoside phosphorylase (NCBI ptt file) 91, 200
CAC1766 CAC1766 Predicted sigma factor (NCBI ptt file) 200, 236
CAC1983 CAC1983 Hypothetical protein (NCBI ptt file) 200, 318
CAC2406 CAC2406 Predicted permease, possible O-antigen transporter (NCBI ptt file) 168, 200
CAC2433 CAC2433 HtrA-like serine protease (with PDZ domain) (NCBI ptt file) 200, 318
CAC2458 CAC2458 2-oxoacid ferredoxin oxidoreductase, beta subunit (NCBI ptt file) 41, 200
CAC2529 CAC2529 Predicted acetyltransferase (NCBI ptt file) 200, 274
CAC2531 CAC2531 S-adenosylmethionine-dependent methyltransferase (NCBI ptt file) 7, 200
CAC2577 CAC2577 GGDEF domain containing protein, (inactivated) (NCBI ptt file) 168, 200
CAC2722 CAC2722 RCC1 repeats protein (beta propeller fold) (NCBI ptt file) 7, 200
CAC2745 CAC2745 Membrane associated methyl-accepting chemotaxis protein (NCBI ptt file) 208, 236
CAC2936 CAC2936 Alpha/beta superfamily hydrolase (NCBI ptt file) 236, 360
CAC3189 clpC ATPases with chaperone activity clpC, two ATP-binding domain (NCBI ptt file) 172, 200
CAC3298 bdhB NADH-dependent butanol dehydrogenase B (BDH II) (NCBI ptt file) 172, 200
CAC3343 CAC3343 Biotin synthase related domain containing protein (NCBI ptt file) 9, 236
CAC3344 CAC3344 Uncharacterized protein, homolog of hypothetical protein (GI:5918205) from Pseudomonas stutzeri (NCBI ptt file) 165, 236
CAC3356 CAC3356 Lactoylglutathione lyase (LGUL) family protein, diverged (NCBI ptt file) 236, 360
CAC3507 CAC3507 Transcriptional regulator, MerR family (NCBI ptt file) 236, 265
CAC3604 ilvD Dihydroxyacid dehydratase (NCBI ptt file) 236, 288
CAC3605 gntP High affinity gluconate/L-idonate permease (NCBI ptt file) 236, 288
CAC3688 CAC3688 Membrane-associated methyl-accepting chemotaxis protein with HAMP domain (NCBI ptt file) 165, 236
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 CAC1766
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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