Organism : Clostridium acetobutylicum | Module List :
CAC0284

Transcriptional regulatory protein, Sir2 family (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
NAD-dependent protein deacetylases, SIR2 family cog/ cog
DNA binding go/ molecular_function
chromatin silencing complex go/ cellular_component
chromatin silencing go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0284
(Mouseover regulator name to see its description)

CAC0284 is regulated by 22 influences and regulates 22 modules.
Regulators for CAC0284 (22)
Regulator Module Operator
CAC0189 343 tf
CAC0255 343 tf
CAC0284 343 tf
CAC0382 343 tf
CAC0474 343 tf
CAC0569 343 tf
CAC0832 343 tf
CAC0863 343 tf
CAC0933 343 tf
CAC1695 343 tf
CAC2143 343 tf
CAC3472 343 tf
CAC0144 6 tf
CAC0183 6 tf
CAC0201 6 tf
CAC0284 6 tf
CAC0474 6 tf
CAC0821 6 tf
CAC0849 6 tf
CAC1766 6 tf
CAC2143 6 tf
CAC2394 6 tf

Warning: CAC0284 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
6666 2.20e-06 gGGaaGtG
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6667 1.40e+04 ACCCAC
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7338 1.50e-04 GgAggGA
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7339 2.50e+03 aAAGGgTagAGAAGT
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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 CAC0284

CAC0284 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
NAD-dependent protein deacetylases, SIR2 family cog/ cog
DNA binding go/ molecular_function
chromatin silencing complex go/ cellular_component
chromatin silencing go/ biological_process
Module neighborhood information for CAC0284

CAC0284 has total of 42 gene neighbors in modules 6, 343
Gene neighbors (42)
Gene Common Name Description Module membership
CAC0088 CAC0088 Peptide methionine sulfoxide reductase (NCBI ptt file) 243, 343
CAC0089 serA D-3 phosphoglycerate dehydrogenase (NCBI ptt file) 109, 343
CAC0183 CAC0183 Transcriptional regulators of NagC/XylR (ROK) family, sugar kinase (NCBI ptt file) 6, 316
CAC0189 CAC0189 Similar to transcriptional regulator, GntR family (NCBI ptt file) 241, 343
CAC0221 CAC0221 Aspartate aminotransferase (NCBI ptt file) 342, 343
CAC0284 CAC0284 Transcriptional regulatory protein, Sir2 family (NCBI ptt file) 6, 343
CAC0318 CAC0318 Membrane permease, predicted cation efflux pumps (NCBI ptt file) 6, 338
CAC0319 CAC0319 ABC transporter ATP-binding protein (NCBI ptt file) 6, 342
CAC0396 CAC0396 3-hexulose-6-phosphate synthase (D-arabino-3-hexulose-6-phosphate formaldehyde lyase) (NCBI ptt file) 343, 357
CAC0426 CAC0426 Transcriptional regulator (HTH_ARAC-domain) (NCBI ptt file) 43, 343
CAC0454 CAC0454 Predicted ATP transporter permease component (NCBI ptt file) 343, 359
CAC0512 CAC0512 Uncharacterized conserved protein, YbhK/UPF0052 family (NCBI ptt file) 41, 343
CAC0867 CAC0867 Putative permease, ortholog yfkN B.subtilis (NCBI ptt file) 226, 343
CAC0959 clpB ATPase with chaperone activity, two ATP-binding domains (NCBI ptt file) 6, 41
CAC1008 CAC1008 Hypothetical protein, CF-30 family (NCBI ptt file) 43, 343
CAC1051 CAC1051 Uncharacterized conserved protein (possible membrane) (NCBI ptt file) 6, 172
CAC1052 CAC1052 Membrane protease subunit, stomatin/prohibitin homolog (NCBI ptt file) 6, 172
CAC1408 CAC1408 Phospho-beta-glucosidase (NCBI ptt file) 79, 343
CAC1518 CAC1518 ABC-type transport system, ATPase component (NCBI ptt file) 111, 343
CAC1700 CAC1700 Response regulator (CheY-like receiver domain and DNA-binding HTH domain) (NCBI ptt file) 6, 14
CAC1722 def N-formylmethionyl-tRNA deformylase (NCBI ptt file) 6, 159
CAC1727 CAC1727 Protein serine/threonine phosphatases, PP2C family (YLOO B.subtilis ortholog) (NCBI ptt file) 6, 271
CAC1742 pta Phosphotransacetylase (NCBI ptt file) 10, 343
CAC1743 askA Acetate kinase (NCBI ptt file) 335, 343
CAC1952 CAC1952 Hypothetical protein (NCBI ptt file) 19, 343
CAC2142 CAC2142 Hypothetical protein (NCBI ptt file) 6, 14
CAC2146 flhF Flagellar GTP-binding protein, FlhF (NCBI ptt file) 6, 14
CAC2153 flbD Flagellar protein flbD (NCBI ptt file) 126, 343
CAC2378 dapA Dihydrodipicolinate synthase (NCBI ptt file) 10, 343
CAC2379 dapB Dihydrodipicolinate reductase (NCBI ptt file) 148, 343
CAC2416 CAC2416 Uncharacterized protein, ErfK family; contains peptidoglycan-binding domain (NCBI ptt file) 6, 263
CAC2685 CAC2685 Trehalose/maltose hydrolase (phosphorylase) (NCBI ptt file) 6, 14
CAC2707 CAC2707 8-oxoguanine-DNA-glycosylase (NCBI ptt file) 98, 343
CAC2731 CAC2731 Predicted permease (NCBI ptt file) 98, 343
CAC2920 tenI Thiamine monophosphate synthase (NCBI ptt file) 6, 316
CAC2922 thiG Uncharacterized enzyme of thiazol biosynthesis (NCBI ptt file) 6, 316
CAC3309 CAC3309 Predicted membrane protein (NCBI ptt file) 6, 19
CAC3353 CAC3353 Hypothetical protein (NCBI ptt file) 6, 327
CAC3384 CAC3384 Protein chain release factor B (NCBI ptt file) 343, 359
CAC3469 CAC3469 Endoglucanase family 5; S-layer homology, cell-adhesion and dockerin domains (NCBI ptt file) 148, 343
CAC3576 CAC3576 Dioxygenase related to 2-nitropropane dioxygenase (NCBI ptt file) 6, 291
CAC3702 CAC3702 Hypothetical protein, CF-7 family (NCBI ptt file) 43, 343
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 CAC0284
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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