Organism : Clostridium acetobutylicum | Module List :
CAC3338

Predicted transcriptional regulator (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
Predicted transcriptional regulators cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3338
(Mouseover regulator name to see its description)

CAC3338 is regulated by 24 influences and regulates 9 modules.
Regulators for CAC3338 (24)
Regulator Module Operator
CAC0162 182 tf
CAC0445 182 tf
CAC0459 182 tf
CAC0876 182 tf
CAC0951 182 tf
CAC1451 182 tf
CAC1465 182 tf
CAC1675 182 tf
CAC1682 182 tf
CAC1945 182 tf
CAC1965 182 tf
CAC2568 182 tf
CAC2768 182 tf
CAC3338 182 tf
CAC0863 31 tf
CAC0876 31 tf
CAC0951 31 tf
CAC1032 31 tf
CAC1469 31 tf
CAC1668 31 tf
CAC1675 31 tf
CAC2546 31 tf
CAC2966 31 tf
CAC3338 31 tf

Warning: CAC3338 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
6716 3.20e-03 aGgaGaGg
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6717 3.00e+03 GGGcACC
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7016 5.70e-14 aaGgGtGA
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7017 7.10e+03 aAggtGaGtgGctT
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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 CAC3338

CAC3338 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted transcriptional regulators cog/ cog
Module neighborhood information for CAC3338

CAC3338 has total of 42 gene neighbors in modules 31, 182
Gene neighbors (42)
Gene Common Name Description Module membership
CAC0076 CAC0076 Predicted permease (NCBI ptt file) 31, 262
CAC0087 CAC0087 Predicted Co/Zn/Cd cation transporter (NCBI ptt file) 182, 206
CAC0116 CAC0116 Carbone-monoxide dehydrogenase, beta chain (NCBI ptt file) 20, 182
CAC0217 pheA Prephenate dehydrotase (pheA) (NCBI ptt file) 182, 292
CAC0310 abrB Regulators of stationary/sporulation gene expression, abrB B.subtilis ortholog (NCBI ptt file) 31, 303
CAC0321 CAC0321 Response regulator (CheY-like domain, HTH domain) (NCBI ptt file) 182, 206
CAC0438 CAC0438 Predicted metal-binding protein (NCBI ptt file) 182, 325
CAC0499 CAC0499 Carboxyl-terminal protease (NCBI ptt file) 182, 233
CAC0500 CAC0500 Membrane protein containing C-terminal PDZ domain (NCBI ptt file) 152, 182
CAC0548 CAC0548 Predicted metal-dependent hydrolase (NCBI ptt file) 27, 31
CAC0869 CAC0869 Thioredoxine reductase (NCBI ptt file) 31, 209
CAC0969 CAC0969 Hypothetical protein (NCBI ptt file) 152, 182
CAC1033 CAC1033 Hypothetical protein, CF-31 family (NCBI ptt file) 87, 182
CAC1050 nadE NH(3)-dependent NAD(+) synthetase (NCBI ptt file) 31, 276
CAC1063 CAC1063 TPR-repeat-containing protein (NCBI ptt file) 31, 182
CAC1262 CAC1262 Predicted nucleotidyltransferases of NarD/TagD family (N-term. domain) , yqeJ ortholog (NCBI ptt file) 31, 238
CAC1325 CAC1325 Uncharacterized conserved protein, YitT (B.subtilis) family (NCBI ptt file) 27, 31
CAC1386 CAC1386 Zn-dependent hydrolases, glyoxylase family (NCBI ptt file) 182, 292
CAC1587 CAC1587 Integral membrane protein possibly involved in chromosome condensation (NCBI ptt file) 134, 182
CAC1675 CAC1675 Predicted transcriptional regulator (HTH winged helix type) (NCBI ptt file) 31, 83
CAC1764 CAC1764 Predicted glutamine amidotransferase (NCBI ptt file) 31, 209
CAC1797 gcpE GcpE protein (NCBI ptt file) 87, 182
CAC2064 deoD Purine nucleoside phosphorylase (NCBI ptt file) 182, 238
CAC2070 CAC2070 Hypothetical protein (NCBI ptt file) 31, 162
CAC2637 lonA ATP-dependent Lon protease (NCBI ptt file) 31, 182
CAC2659 CAC2659 Putative stress-responsive transcriptional regulator PspC (NCBI ptt file) 31, 162
CAC2738 CAC2738 Uncharacterized conserved protein (NCBI ptt file) 31, 262
CAC2778 CAC2778 Rubredoxin (NCBI ptt file) 31, 259
CAC3028 CAC3028 Conserved membrane protein, possible homolog of CAAX-like membrane endopeptidase (NCBI ptt file) 31, 206
CAC3073 CAC3073 Sugar transferase involved in lipopolysaccharide synthesis (NCBI ptt file) 25, 31
CAC3233 CAC3233 Uncharacterized conserved protein, YITC B.subtilis ortholog (NCBI ptt file) 31, 182
CAC3289 CAC3289 Iron-regulated ABC-type transporter membrane component (SufB) (NCBI ptt file) 31, 182
CAC3306 CAC3306 Thiol peroxidase, TPX (NCBI ptt file) 87, 182
CAC3328 CAC3328 Predicted membrane protein (NCBI ptt file) 10, 182
CAC3338 CAC3338 Predicted transcriptional regulator (NCBI ptt file) 31, 182
CAC3464 CAC3464 Uncharacterized conserved protein (fragment) (NCBI ptt file) 182, 206
CAC3556 CAC3556 Probable S-layer protein (NCBI ptt file) 31, 93
CAC3569 accD Acetyl-CoA carboxylase beta subunit (NCBI ptt file) 182, 239
CAC3580 CAC3580 Dioxygenase related to 2-nitropropane dioxygenase (NCBI ptt file) 31, 276
CAC3595 CAC3595 Uncharacterized FAD-dependent dehydrogenase (NCBI ptt file) 182, 292
CAC3718 CAC3718 Exopolyphosphatase-like domain and PAS domain containing protein, YYBT B.subtilis ortholog (NCBI ptt file) 182, 298
CAC3719 CAC3719 Uncharacterized predicted membrane protein, YYBS B.subtilis homolog (NCBI ptt file) 182, 298
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 CAC3338
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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