Organism : Clostridium acetobutylicum | Module List :
CAC3037 ccpA

Catabolite control protein, LacI family transcriptional regulator (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
alanine racemase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3037
(Mouseover regulator name to see its description)

CAC3037 is regulated by 21 influences and regulates 20 modules.
Regulators for CAC3037 ccpA (21)
Regulator Module Operator
CAC0255 209 tf
CAC0745 209 tf
CAC0821 209 tf
CAC1300 209 tf
CAC1426 209 tf
CAC1668 209 tf
CAC1766 209 tf
CAC2052 209 tf
CAC2394 209 tf
CAC2552 209 tf
CAC2842 209 tf
CAC3037 209 tf
CAC3063 209 tf
CAC3324 209 tf
CAC0977 11 tf
CAC1264 11 tf
CAC1469 11 tf
CAC1668 11 tf
CAC2071 11 tf
CAC2236 11 tf
CAC3037 11 tf

Warning: CAC3037 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
6676 3.10e-02 AAGGgGG
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6677 1.50e+04 GGGtAGG
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7070 7.00e+01 CAacaGGcGg
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7071 7.60e+03 CGGtCc
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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 CAC3037

CAC3037 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
alanine racemase activity go/ molecular_function
Module neighborhood information for CAC3037

CAC3037 has total of 45 gene neighbors in modules 11, 209
Gene neighbors (45)
Gene Common Name Description Module membership
CAC0187 nagB Glucosamine-6-phosphate isomerase (glucosamine-6-phosphate deaminase) (gene nagB) (NCBI ptt file) 11, 215
CAC0315 CAC0315 Predicted acetyltransferase (NCBI ptt file) 11, 206
CAC0350 CAC0350 Hypothetical protein (NCBI ptt file) 11, 179
CAC0815 CAC0815 Methyl-accepting chemotaxis protein (NCBI ptt file) 134, 209
CAC0816 CAC0816 Lipase-esterase related protein (NCBI ptt file) 176, 209
CAC0869 CAC0869 Thioredoxine reductase (NCBI ptt file) 31, 209
CAC0982 CAC0982 Hypothetical protein (NCBI ptt file) 209, 266
CAC0997 ndk Probable nucleoside-diphosphate kinase N-terminal domain (NCBI ptt file) 11, 162
CAC1013 CAC1013 FTSA related protein, predicted ATPases of the HSP70 family (NCBI ptt file) 11, 306
CAC1039 CAC1039 Membrane protein, TerC homolog (NCBI ptt file) 11, 266
CAC1265 CAC1265 Translation initiation inhibitor, yabJ B.subtilis ortholog (NCBI ptt file) 11, 221
CAC1357 CAC1357 Uncharacterized predicted metal-binding protein (NCBI ptt file) 11, 99
CAC1669 CstA Carbon starvation protein (NCBI ptt file) 209, 238
CAC1764 CAC1764 Predicted glutamine amidotransferase (NCBI ptt file) 31, 209
CAC1854 CAC1854 Nudix (MutT) family hydrolase (NCBI ptt file) 209, 277
CAC1914 CAC1914 Hypothetical protein (NCBI ptt file) 11, 53
CAC2004 CAC2004 Siderophore/Surfactin synthetase related protein (NCBI ptt file) 60, 209
CAC2007 CAC2007 Predicted glycosyltransferase (NCBI ptt file) 97, 209
CAC2011 fabH Possible 3-oxoacyl-[acyl-carrier-protein] synthase III (NCBI ptt file) 97, 209
CAC2016 fadB Enoyl-CoA hydratase (NCBI ptt file) 97, 209
CAC2017 CAC2017 Acyl carrier protein (NCBI ptt file) 134, 209
CAC2018 CAC2018 Aldehyde:ferredoxin oxidoreductase (NCBI ptt file) 134, 209
CAC2021 moeA Molybdopterin biosynthesis enzyme, MoeA (short form) (NCBI ptt file) 133, 209
CAC2022 moaB Molybdopterin biosynthesis enzyme, moaB (NCBI ptt file) 209, 282
CAC2025 CAC2025 Hypothetical protein (NCBI ptt file) 209, 282
CAC2121 CAC2121 Predicted enzyme with a TIM-barrel fold (NCBI ptt file) 11, 201
CAC2130 spoVD Stage V sporulation protein D, spoVD, FtsI/pbp family (NCBI ptt file) 11, 29
CAC2133 CAC2133 Uncharacterized conserved protein, YLLB B.subtilis family (NCBI ptt file) 11, 53
CAC2182 CAC2182 Hypothetical protein (NCBI ptt file) 209, 348
CAC2236 CAC2236 Uncharacterized conserved protein of YjeB/RRF2 family (NCBI ptt file) 11, 25
CAC2446 CAC2446 Hypothetical protein (NCBI ptt file) 27, 209
CAC2449 CAC2449 Predicted flavoprotein (NCBI ptt file) 11, 80
CAC2489 CAC2489 Predicted membrane protein (NCBI ptt file) 11, 26
CAC2613 glcK Transcriptional regulators of NagC/XylR family (NCBI ptt file) 11, 147
CAC2681 CAC2681 Hypothetical protein (NCBI ptt file) 11, 325
CAC2775 CAC2775 Phosphohydrolase from calcineurin family (NCBI ptt file) 11, 231
CAC3034 CAC3034 MutS-like mismatch repair protein, ATPases (NCBI ptt file) 11, 215
CAC3037 ccpA Catabolite control protein, LacI family transcriptional regulator (NCBI ptt file) 11, 209
CAC3266 CAC3266 Hypothetical protein (NCBI ptt file) 11, 99
CAC3279 CAC3279 Possible surface protein, responsible for cell interaction; contains cell adhesion domain and ChW-repeats (NCBI ptt file) 209, 261
CAC3290 CAC3290 Iron-regulated ABC-type transporter membrane component (SufB) (NCBI ptt file) 201, 209
CAC3291 CAC3291 Selenocysteine lyase, NifS family (NCBI ptt file) 209, 296
CAC3292 CAC3292 NifU homolog involved in Fe-S cluster formation (NCBI ptt file) 209, 277
CAC3315 htpG Molecular chaperone, HSP90 family (NCBI ptt file) 11, 244
CAC3592 CAC3592 Hypothetical protein, CF-27 family (NCBI ptt file) 92, 209
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 CAC3037
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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