Organism : Clostridium acetobutylicum | Module List :
CAC1928

Hypothetical protein (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
zinc ion binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1928
(Mouseover regulator name to see its description)

CAC1928 is regulated by 14 influences and regulates 16 modules.
Regulators for CAC1928 (14)
Regulator Module Operator
CAC1867 54 tf
CAC1900 54 tf
CAC1915 54 tf
CAC1928 54 tf
CAC1941 54 tf
CAC2966 54 tf
CAC3406 54 tf
CAC0254 175 tf
CAC0255 175 tf
CAC1226 175 tf
CAC1698 175 tf
CAC1915 175 tf
CAC1928 175 tf
CAC1941 175 tf

Warning: CAC1928 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
6762 7.60e+01 AAGgAG
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6763 8.60e+01 TTtcaaAtatAGTaagCTaATG
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7002 6.10e+01 GcAGGAT
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7003 4.00e+02 TggA.GaGgaT
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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 CAC1928

CAC1928 is enriched for 3 functions in 2 categories.
Enrichment Table (3)
Function System
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
zinc ion binding go/ molecular_function
Module neighborhood information for CAC1928

CAC1928 has total of 36 gene neighbors in modules 54, 175
Gene neighbors (36)
Gene Common Name Description Module membership
CAC0020 CAC0020 MDR-type permease (NCBI ptt file) 98, 175
CAC0829 CAC0829 Uncharacterized conserved membrane protein, similar to MDR (VANZ) ORF of Enterococcus (NCBI ptt file) 98, 175
CAC1872 repB Replication initiation protein REP (NCBI ptt file) 54, 342
CAC1895 CAC1895 Phage terminase-like protein, large subunit (NCBI ptt file) 54, 332
CAC1900 CAC1900 Phage regulatory Com-like protein, containing Zn-finger (NCBI ptt file) 54, 171
CAC1901 CAC1901 Hypothetical protein (NCBI ptt file) 54, 342
CAC1915 CAC1915 Hypothetical protein (NCBI ptt file) 54, 175
CAC1916 CAC1916 Hypothetical protein (NCBI ptt file) 54, 332
CAC1917 CAC1917 Hypothetical protein (NCBI ptt file) 54, 175
CAC1918 CAC1918 Hypothetical protein (NCBI ptt file) 54, 332
CAC1919 CAC1919 Phage related SSB-like protein (NCBI ptt file) 101, 175
CAC1920 CAC1920 Zn-finger containing protein (NCBI ptt file) 54, 246
CAC1921 CAC1921 Hypothetical protein (NCBI ptt file) 54, 117
CAC1923 CAC1923 Hypothetical protein (NCBI ptt file) 54, 175
CAC1924 CAC1924 Hypothetical protein (NCBI ptt file) 101, 175
CAC1927 CAC1927 Hypothetical protein, CF-31 family (NCBI ptt file) 101, 175
CAC1928 CAC1928 Hypothetical protein (NCBI ptt file) 54, 175
CAC1929 CAC1929 Hypothetical protein (NCBI ptt file) 101, 175
CAC1930 CAC1930 Uncharacterized protein, MazG family (NCBI ptt file) 175, 311
CAC1931 CAC1931 Hypothetical protein (NCBI ptt file) 54, 175
CAC1934 CAC1934 Hypothetical protein (NCBI ptt file) 54, 284
CAC1935 CAC1935 Hypothetical protein (NCBI ptt file) 139, 175
CAC1936 CAC1936 Hypothetical protein (NCBI ptt file) 101, 175
CAC1937 CAC1937 Hypothetical protein (NCBI ptt file) 54, 284
CAC1938 CAC1938 Predicted HD superfamily hydrolase (NCBI ptt file) 54, 284
CAC1939 CAC1939 Hypothetical protein (NCBI ptt file) 54, 366
CAC1942 CAC1942 Hypothetical protein (NCBI ptt file) 54, 342
CAC1944 CAC1944 Hypothetical protein (NCBI ptt file) 54, 332
CAC1945 CAC1945 Phage related anti-repressor protein (NCBI ptt file) 54, 171
CAC2100 CAC2100 Hypothetical protein (NCBI ptt file) 54, 282
CAC2101 CAC2101 Hypothetical protein (NCBI ptt file) 54, 333
CAC2102 CAC2102 Prepilin peptidase (NCBI ptt file) 54, 312
CAC2103 CAC2103 General secretion pathway protein, pilin family (NCBI ptt file) 54, 320
CAC2104 CAC2104 General secretion pathway protein F (NCBI ptt file) 54, 282
CAC2106 CAC2106 Predicted membrane protein (NCBI ptt file) 54, 282
CAC3498 CAC3498 Sugar kinase, ribokinase family (NCBI ptt file) 98, 175
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 CAC1928
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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