Organism : Clostridium acetobutylicum | Module List :
CAC1300 sigA

RNA polymerase sigma factor RPOD (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) cog/ cog
sequence-specific DNA binding transcription factor 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
RpoD_Cterm tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1300
(Mouseover regulator name to see its description)

CAC1300 is regulated by 24 influences and regulates 11 modules.
Regulators for CAC1300 sigA (24)
Regulator Module Operator
CAC0197 159 tf
CAC0310 159 tf
CAC0514 159 tf
CAC0821 159 tf
CAC1300 159 tf
CAC1469 159 tf
CAC1719 159 tf
CAC1800 159 tf
CAC1950 159 tf
CAC2143 159 tf
CAC2259 159 tf
CAC2934 159 tf
CAC3267 159 tf
CAC0627 256 tf
CAC1032 256 tf
CAC1300 256 tf
CAC1675 256 tf
CAC1766 256 tf
CAC1800 256 tf
CAC1950 256 tf
CAC2634 256 tf
CAC3166 256 tf
CAC3199 256 tf
CAC3669 256 tf

Warning: CAC1300 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
6970 2.00e-02 TCCTca
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6971 1.50e+03 gaatcaAgGatGGA
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7164 6.00e-01 gGaGtGc
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7165 1.20e+04 GgCAaAGG
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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 CAC1300

CAC1300 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) cog/ cog
sequence-specific DNA binding transcription factor 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
RpoD_Cterm tigr/ tigrfam
Module neighborhood information for CAC1300

CAC1300 has total of 48 gene neighbors in modules 159, 256
Gene neighbors (48)
Gene Common Name Description Module membership
CAC0018 CAC0018 Putative NADPH-quinone reductase, YabF family (NCBI ptt file) 256, 327
CAC0365 CAC0365 Phosphoglycerate dehydrogenase (NCBI ptt file) 256, 316
CAC0367 rocB Arginine degradation protein (gene rocB) (NCBI ptt file) 256, 271
CAC0376 CAC0376 N-dimethylarginine dimethylaminohydrolase (similar to ykgA B.subtilis) (NCBI ptt file) 111, 256
CAC0377 CAC0377 Amino acid (glutamine) ABC transporter, permease component (NCBI ptt file) 172, 256
CAC0574 CAC0574 Pectate lyase H (FS) (NCBI ptt file) 123, 256
CAC0998 CAC0998 Homoserine dehydrogenase (NCBI ptt file) 234, 256
CAC0999 thrC Threonine synthase (NCBI ptt file) 234, 256
CAC1000 CAC1000 Uncharacterized protein, homolog of yhfF B.subtilis (NCBI ptt file) 256, 327
CAC1089 CAC1089 Serine kinase/phosphatase HPr (NCBI ptt file) 26, 159
CAC1090 CAC1090 5-formyltetrahydrofolate cyclo-ligase (NCBI ptt file) 159, 229
CAC1091 CAC1091 Aspartyl aminopeptidase (NCBI ptt file) 159, 234
CAC1260 obg SPO0B-associated GTPase, obg (NCBI ptt file) 172, 256
CAC1261 CAC1261 Predicted RNA-binding protein containing KH domain (NCBI ptt file) 172, 256
CAC1300 sigA RNA polymerase sigma factor RPOD (NCBI ptt file) 159, 256
CAC1303 CAC1303 Uncharacterized protein of YbgI/Acr family (NCBI ptt file) 10, 159
CAC1352 CAC1352 Membrane associated chemotaxis sensory transducer protein (MSP domain and HAMP domain) (NCBI ptt file) 137, 256
CAC1427 gabT 4-aminobutyrate aminotransferase (PLP-dependent) (NCBI ptt file) 111, 256
CAC1715 CAC1715 PLP-dependent aminotransferase (NCBI ptt file) 159, 234
CAC1722 def N-formylmethionyl-tRNA deformylase (NCBI ptt file) 6, 159
CAC1723 fmt Methionyl-tRNA formyltransferase (NCBI ptt file) 159, 329
CAC1724 CAC1724 Predicted metal-dependent peptidase (NCBI ptt file) 159, 329
CAC1725 CAC1725 Predicted rRNA methylase, SUN family (NCBI ptt file) 159, 315
CAC1828 CAC1828 TldD protein fragment (NCBI ptt file) 159, 172
CAC1835 miaA TRNA delta(2)-isopentenylpyrophosphate transferase (NCBI ptt file) 159, 273
CAC1836 mutL DNA mismatch repair enzyme, MutL (NCBI ptt file) 36, 159
CAC1837 mutS Mismatch repair protein MutS, ATPase (NCBI ptt file) 159, 172
CAC1838 CAC1838 Predicted Fe-S oxidoreductase, YMCB B.subtilis ortholog (NCBI ptt file) 36, 159
CAC2077 CAC2077 Deoxyxylulose-5-phosphate synthase (NCBI ptt file) 159, 229
CAC2081 xseB Exonuclease VII small subunit (NCBI ptt file) 159, 310
CAC2105 CAC2105 General secretion pathway protein E, ATPase (NCBI ptt file) 256, 320
CAC2262 addA ATP-dependent exonuclease (exonuclease V) synthesis protein AddA (helicase and exonuclease domains) (NCBI ptt file) 14, 159
CAC2263 addB ATP-dependent exonuclease synthesis protein AddB (superfamily I helicase) (NCBI ptt file) 159, 314
CAC2344 CAC2344 LPS biosynthesis protein , RfbU family (NCBI ptt file) 137, 159
CAC2351 CAC2351 Glycosyltransferase (NCBI ptt file) 100, 256
CAC2368 CAC2368 Hypothetical protein (NCBI ptt file) 254, 256
CAC2579 CAC2579 Uncharacterized conserved membrane protein (NCBI ptt file) 159, 163
CAC2631 CAC2631 Uncharacterized protein, ErfK family (NCBI ptt file) 159, 273
CAC2642 CAC2642 Predicted endonuclease (NCBI ptt file) 159, 352
CAC2643 CAC2643 Hypothetical protein (NCBI ptt file) 159, 271
CAC2726 CAC2726 Uncharacterized protein, possible ynzC B.subtilis homolog (NCBI ptt file) 159, 298
CAC2882 CAC2882 Predicted translation factor (SUA5) (NCBI ptt file) 79, 256
CAC2885 CAC2885 S-adenosylmethionine-dependent methyltransferase, HEMK ortholog (NCBI ptt file) 229, 256
CAC2886 CAC2886 Uncharacterized conserved protein, predicted metal-dependent enzyme, YQHQ B.subtilis ortholog (NCBI ptt file) 79, 256
CAC2989 CAC2989 PHP superfamily hydrolase, YABD ortholog (NCBI ptt file) 254, 256
CAC3039 CAC3039 Hypothetical secreted protein (NCBI ptt file) 245, 256
CAC3096 thiK Hydroxyethylthiazole kinase ThiM/ThiK (FS!) (NCBI ptt file) 256, 316
CAC3199 CAC3199 NifR3 family enzyme (NCBI ptt file) 79, 256
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 CAC1300
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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