Organism : Clostridium acetobutylicum | Module List :
CAC3267

Specialized sigma subunit of RNA polymerase (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog 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
sigma70-ECF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3267
(Mouseover regulator name to see its description)

CAC3267 is regulated by 18 influences and regulates 17 modules.
Regulators for CAC3267 (18)
Regulator Module Operator
CAC0113 225 tf
CAC1264 225 tf
CAC1451 225 tf
CAC2209 225 tf
CAC2608 225 tf
CAC2634 225 tf
CAC2889 225 tf
CAC3152 225 tf
CAC3443 225 tf
CAC3518 225 tf
CAC3611 225 tf
CAC0174 99 tf
CAC1226 99 tf
CAC2306 99 tf
CAC2546 99 tf
CAC3267 99 tf
CAC3443 99 tf
CAC3646 99 tf

Warning: CAC3267 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
6850 3.20e+01 gAttGGGGgat
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6851 6.70e+02 CGCCcG
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7102 8.80e-08 aaaGGtGatg
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7103 1.00e+03 TgcTttcGcc
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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 CAC3267

CAC3267 is enriched for 6 functions in 3 categories.
Module neighborhood information for CAC3267

CAC3267 has total of 48 gene neighbors in modules 99, 225
Gene neighbors (48)
Gene Common Name Description Module membership
CAC0029 CAC0029 Distantly related to cell wall-associated hydrolases, similar to yycO Bacillus subtilis (NCBI ptt file) 67, 99
CAC0030 CAC0030 Hypothetical protein (NCBI ptt file) 67, 99
CAC0043 CAC0043 Hypothetical protein, CF-3 family (NCBI ptt file) 99, 312
CAC0085 CAC0085 Hypothetical protein (NCBI ptt file) 60, 99
CAC0229 CAC0229 Predicted Zn-dependent proteases, TLDD ortholog (NCBI ptt file) 91, 225
CAC0230 CAC0230 Inactivated predicted Zn-dependent protease, PMBA ortholog (NCBI ptt file) 91, 225
CAC0270 CAC0270 Hypothetical protein (NCBI ptt file) 67, 225
CAC0323 CAC0323 Sensory transduction histidine kinase (NCBI ptt file) 99, 147
CAC0375 patA PLP-dependent aminotransferase (gene patA) (NCBI ptt file) 99, 113
CAC0433 CAC0433 Methyl-accepting chemotaxis protein (NCBI ptt file) 20, 225
CAC0452 CAC0452 Permease (NCBI ptt file) 99, 109
CAC0482 CAC0482 Zn-dependent hydrolases of the metallo-beta-lactamase superfamily (NCBI ptt file) 225, 239
CAC0488 CAC0488 Hypothetical protein (NCBI ptt file) 99, 248
CAC0603 CAC0603 Superfamily I DNA and RNA helicase (NCBI ptt file) 91, 225
CAC0825 CAC0825 Endoglucanase family 5 (NCBI ptt file) 225, 261
CAC0891 CAC0891 Hypothetical protein (NCBI ptt file) 99, 252
CAC0945 ssb Single-stranded DNA-binding protein (NCBI ptt file) 63, 99
CAC1098 polA DNA polymerase I, polA (NCBI ptt file) 99, 109
CAC1357 CAC1357 Uncharacterized predicted metal-binding protein (NCBI ptt file) 11, 99
CAC1544 CAC1544 Cytidine deaminase, cdd (NCBI ptt file) 91, 225
CAC1586 CAC1586 Integral membrane protein possibly involved in chromosome condensation (NCBI ptt file) 29, 99
CAC1873 CAC1873 Hypothetical protein (NCBI ptt file) 99, 162
CAC1909 rnd Ribonuclease D (NCBI ptt file) 225, 277
CAC1910 CAC1910 Predicted membrane protein (NCBI ptt file) 225, 277
CAC2033 CAC2033 Hypothetical protein (NCBI ptt file) 99, 312
CAC2139 flgG Flagellar basal body rod protein (NCBI ptt file) 192, 225
CAC2337 CAC2337 Phosphomannomutase (NCBI ptt file) 225, 294
CAC2450 CAC2450 Desulfoferrodoxin (NCBI ptt file) 80, 225
CAC2601 CAC2601 S-adenosylmethionine decarboxylase (NCBI ptt file) 82, 225
CAC2634 CAC2634 Ferric uptake regulator (FUR family), YGAG B.subtilis ortholog (NCBI ptt file) 49, 225
CAC2658 glnA Glutamine synthetase type III (NCBI ptt file) 99, 106
CAC2725 CAC2725 Predicted hydrolase from alpha/beta family, YQKD B.subtilis ortholog (NCBI ptt file) 51, 225
CAC2785 CAC2785 Hypothetical protein (NCBI ptt file) 134, 225
CAC2897 CAC2897 Predicted UDP-glucuronosyltransferase, YPFP B/subtilis ortholog (NCBI ptt file) 225, 286
CAC2914 panB Ketopantoate hydroxymethyltransferase (NCBI ptt file) 225, 235
CAC3085 CAC3085 TPR-repeat-containing protein; Cell-adhesion domain (NCBI ptt file) 225, 344
CAC3086 CAC3086 Protein containing cell adhesion domain (NCBI ptt file) 225, 344
CAC3248 CAC3248 Hypothetical protein (NCBI ptt file) 157, 225
CAC3249 CAC3249 Hypothetical protein (NCBI ptt file) 157, 225
CAC3251 CAC3251 Sensory transduction protein containing HD_GYP domain (NCBI ptt file) 63, 225
CAC3265 CAC3265 Predicted membrane protein (NCBI ptt file) 13, 99
CAC3266 CAC3266 Hypothetical protein (NCBI ptt file) 11, 99
CAC3267 CAC3267 Specialized sigma subunit of RNA polymerase (NCBI ptt file) 99, 225
CAC3460 CAC3460 Hypothetical protein, CF-28 family (NCBI ptt file) 60, 99
CAC3518 CAC3518 Transcriptional regulators, AcrR family (NCBI ptt file) 225, 359
CAC3570 accC Biotin carboxylase (NCBI ptt file) 44, 225
CAC3577 acp Acyl Carrier Protein, ACP (NCBI ptt file) 91, 225
CAC3596 pgsA Phosphatidylglycerophosphate synthase (NCBI ptt file) 13, 99
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 CAC3267
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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