Organism : Clostridium acetobutylicum | Module List :
CAC1469

Iron-dependent transcription repressor (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Mn-dependent transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
iron ion binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1469
(Mouseover regulator name to see its description)

CAC1469 is regulated by 24 influences and regulates 30 modules.
Regulators for CAC1469 (24)
Regulator Module Operator
CAC0422 114 tf
CAC0550 114 tf
CAC0863 114 tf
CAC1404 114 tf
CAC1469 114 tf
CAC2430 114 tf
CAC2794 114 tf
CAC3475 114 tf
CAC3487 114 tf
CAC3606 114 tf
CAC0231 127 tf
CAC0299 127 tf
CAC0310 127 tf
CAC0693 127 tf
CAC0863 127 tf
CAC0951 127 tf
CAC1032 127 tf
CAC1469 127 tf
CAC2236 127 tf
CAC2990 127 tf
CAC3267 127 tf
CAC3606 127 tf
CAC3669 127 tf
CAC3677 127 tf

Warning: CAC1469 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
6880 7.50e+01 aaGAGggataA
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6881 3.20e+02 CCActcaAcC
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6906 1.20e-02 TcCcTcCT
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6907 4.50e+03 GcTacTACcGC
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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 CAC1469

CAC1469 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Mn-dependent transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
iron ion binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for CAC1469

CAC1469 has total of 33 gene neighbors in modules 114, 127
Gene neighbors (33)
Gene Common Name Description Module membership
CAC0138 CAC0138 ABC transporter, ATP-binding component (NCBI ptt file) 36, 114
CAC0139 CAC0139 Predicted permease (NCBI ptt file) 36, 114
CAC0140 CAC0140 Predicted permease (NCBI ptt file) 67, 114
CAC0141 CAC0141 Membrane permease, predicted cation efflux pumps (NCBI ptt file) 36, 114
CAC0742 CAC0742 Uncharacterized protein, containing predicted phosphatase domain (NCBI ptt file) 81, 127
CAC0861 CAC0861 ABC-type multidrug transport system, ATPase component (NCBI ptt file) 81, 127
CAC0970 CAC0970 Isopropylmalate synthase (NCBI ptt file) 114, 127
CAC0971 citB Aconitase A (NCBI ptt file) 114, 127
CAC0972 citC Isocitrate dehydrogenase (NCBI ptt file) 114, 127
CAC1336 CAC1336 Hypothetical protein (NCBI ptt file) 114, 127
CAC1337 CAC1337 Spore coat protein COTJB (NCBI ptt file) 114, 127
CAC1338 CAC1338 Spore coat protein COTJC (NCBI ptt file) 114, 127
CAC1431 rpiA Ribose 5-phosphate isomerase (NCBI ptt file) 125, 127
CAC1469 CAC1469 Iron-dependent transcription repressor (NCBI ptt file) 114, 127
CAC1572 CAC1572 Fructose-1,6-bisphosphatase (YYDE B.subtils ortholog) (NCBI ptt file) 100, 114
CAC1633 CAC1633 Protein from bacterioferritin family (NCBI ptt file) 114, 127
CAC1656 CAC1656 Hypothetical protein, CF-39 family (NCBI ptt file) 114, 273
CAC1866 CAC1866 Putative 4-Cys ferredoxin (NCBI ptt file) 114, 127
CAC2135 CAC2135 ATP-dependent serine protease LA/LON family (NCBI ptt file) 127, 139
CAC2243 asnB N-terminal domain of asparagine synthase (NCBI ptt file) 100, 114
CAC2249 CAC2249 C-terminal domain of asparagine synthase (NCBI ptt file) 114, 300
CAC2365 sspA Small acid-soluble spore protein (NCBI ptt file) 19, 127
CAC2747 CAC2747 Protein containing LysM repeats (N-terminal domain) and domain related to chitinase (NCBI ptt file) 114, 127
CAC2797 CAC2797 Hypothetical protein (NCBI ptt file) 114, 127
CAC2909 CAC2909 Spore coat protein cotS related (diverged) (NCBI ptt file) 114, 190
CAC2968 CAC2968 Mannose-1-phosphate guanylyltransferase (NCBI ptt file) 114, 127
CAC2969 CAC2969 3-methyladenine DNA glycosylase (NCBI ptt file) 19, 127
CAC3018 CAC3018 Rubrerythrin (NCBI ptt file) 114, 127
CAC3078 CAC3078 Uncharacterized secreted protein, YBBR Bacillus subtilis homolog (NCBI ptt file) 114, 142
CAC3562 CAC3562 HD superfamily hydrolase (NCBI ptt file) 127, 247
CAC3674 CAC3674 Two CBS domain containing protein (NCBI ptt file) 114, 300
CAC3716 lonB Lon-like ATP-dependent protease (NCBI ptt file) 36, 114
CAC3717 rplI Ribosomal protein L9 (NCBI ptt file) 114, 243
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 CAC1469
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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