Organism : Clostridium acetobutylicum | Module List :
CAC0465

Predicted transcriptional regulator, dicA/hipB/ansR family (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0465
(Mouseover regulator name to see its description)

CAC0465 is regulated by 22 influences and regulates 13 modules.
Regulators for CAC0465 (22)
Regulator Module Operator
CAC0115 10 tf
CAC0360 10 tf
CAC0465 10 tf
CAC0474 10 tf
CAC0514 10 tf
CAC0821 10 tf
CAC2084 10 tf
CAC3424 10 tf
CAC3579 10 tf
CAC3603 10 tf
CAC0032 52 tf
CAC0144 52 tf
CAC0255 52 tf
CAC0265 52 tf
CAC0465 52 tf
CAC1675 52 tf
CAC1766 52 tf
CAC1800 52 tf
CAC2546 52 tf
CAC3142 52 tf
CAC3475 52 tf
CAC3512 52 tf

Warning: CAC0465 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
6674 7.00e-07 aCCtcCct
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6675 7.20e+03 CTGGGAC
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6758 9.90e-02 tTatcaCCTCcaat
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6759 2.00e+03 tAccTgaAtagcta..Tc
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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 CAC0465

CAC0465 is enriched for 1 functions in 2 categories.
Enrichment Table (1)
Function System
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for CAC0465

CAC0465 has total of 39 gene neighbors in modules 10, 52
Gene neighbors (39)
Gene Common Name Description Module membership
CAC0125 dnaX DNA-directed DNA polymerase, III chain (dnaX) (NCBI ptt file) 10, 356
CAC0126 CAC0126 Uncharacterized conserved protein, YbaB family (NCBI ptt file) 10, 281
CAC0198 CAC0198 Uncharacterized membrane protein, ortholog YYAS B.subtilis (NCBI ptt file) 27, 52
CAC0360 CAC0360 Transcriptional regulator, LacI family (HTH lacI domain), B.subtilis degA ortholog (NCBI ptt file) 10, 259
CAC0465 CAC0465 Predicted transcriptional regulator, dicA/hipB/ansR family (NCBI ptt file) 10, 52
CAC0505 CAC0505 Cell division membrane protein (NCBI ptt file) 52, 58
CAC0517 pfk 6-phosphofructokinase (NCBI ptt file) 10, 191
CAC0600 CAC0600 Predicted membrane protein (NCBI ptt file) 10, 71
CAC0606 CAC0606 C-terminal region cation efflux system protein CZCD (NCBI ptt file) 52, 277
CAC0632 CAC0632 Predicted phosphatase (NCBI ptt file) 52, 277
CAC0637 tyrS Tyrosyl-tRNA synthetase (NCBI ptt file) 10, 64
CAC0680 CAC0680 Predicted membrane protein (NCBI ptt file) 52, 59
CAC0709 gapC Glyceraldehyde 3-phosphate dehydrogenase, gene gapC (NCBI ptt file) 10, 20
CAC0983 CAC0983 Hypothetical protein (NCBI ptt file) 52, 277
CAC1171 CAC1171 Hypothetical protein (NCBI ptt file) 52, 262
CAC1173 CAC1173 Hypothetical protein (NCBI ptt file) 52, 262
CAC1301 CAC1301 Predicted membrane protein (NCBI ptt file) 10, 251
CAC1302 CAC1302 Predicted SAM-dependent methyltransferase (NCBI ptt file) 10, 64
CAC1303 CAC1303 Uncharacterized protein of YbgI/Acr family (NCBI ptt file) 10, 159
CAC1742 pta Phosphotransacetylase (NCBI ptt file) 10, 343
CAC2185 CAC2185 Uncharacterized protein, homolog HI1244 from Haemophilus influenzae (NCBI ptt file) 52, 93
CAC2260 CAC2260 Spore coat polysaccharide biosynthesis protein, Pyridoxal-dependent enzyme (NCBI ptt file) 27, 52
CAC2362 thrS Threonyl-tRNA synthetase (NCBI ptt file) 10, 356
CAC2378 dapA Dihydrodipicolinate synthase (NCBI ptt file) 10, 343
CAC2440 CAC2440 Predicted membrane protein (NCBI ptt file) 52, 306
CAC2513 CAC2513 Predicted membrane protein (NCBI ptt file) 52, 132
CAC2680 pgi Glucose-6-phosphate isomerase (NCBI ptt file) 10, 286
CAC2709 etfA Electron transfer flavoprotein alpha-subunit (NCBI ptt file) 10, 59
CAC2836 CAC2836 Zn-binding lipoprotein related (surface adhesin A), ADHS (NCBI ptt file) 52, 277
CAC2873 CAC2873 Acetyl-CoA acetyltransferase (NCBI ptt file) 10, 109
CAC2999 CAC2999 Hypothetical protein (NCBI ptt file) 52, 276
CAC3090 CAC3090 Fumarate hydratase, subunit B (C-terminal domain of FumA E.coli) class I (NCBI ptt file) 10, 79
CAC3250 CAC3250 Possible glutamate racemase (NCBI ptt file) 10, 92
CAC3263 CAC3263 Hypothetical protein (NCBI ptt file) 52, 151
CAC3328 CAC3328 Predicted membrane protein (NCBI ptt file) 10, 182
CAC3362 CAC3362 Uncharacterized conserved membrane protein, YOAK B.subtilis homolog (NCBI ptt file) 52, 147
CAC3365 CAC3365 Hypothetical protein (NCBI ptt file) 10, 92
CAC3366 CAC3366 Hypothetical protein (NCBI ptt file) 10, 92
CAC3401 CAC3401 Predicted membrane protein (NCBI ptt file) 52, 262
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 CAC0465
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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