Organism : Clostridium acetobutylicum | Module List :
CAC0001 dnaA

DNA replication initiator protein, ATPase (NCBI ptt file)

CircVis
Functional Annotations (8)
Function System
ATPase involved in DNA replication initiation cog/ cog
DNA replication origin binding go/ molecular_function
UDP-N-acetylglucosamine diphosphorylase activity go/ molecular_function
ATP binding go/ molecular_function
DNA-dependent DNA replication initiation go/ biological_process
regulation of DNA replication go/ biological_process
nucleoside-triphosphatase activity go/ molecular_function
DnaA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0001
(Mouseover regulator name to see its description)

CAC0001 is regulated by 25 influences and regulates 0 modules.
Regulators for CAC0001 dnaA (25)
Regulator Module Operator
CAC0081 3 tf
CAC0113 3 tf
CAC0201 3 tf
CAC0859 3 tf
CAC1786 3 tf
CAC1799 3 tf
CAC2060 3 tf
CAC2074 3 tf
CAC2084 3 tf
CAC2209 3 tf
CAC2297 3 tf
CAC2939 3 tf
CAC3063 3 tf
CAC3152 3 tf
CAC3166 3 tf
CAC3472 3 tf
CAC0201 5 tf
CAC0768 5 tf
CAC1578 5 tf
CAC2084 5 tf
CAC2254 5 tf
CAC3143 5 tf
CAC3152 5 tf
CAC3166 5 tf
CAC3370 5 tf

Warning: CAC0001 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
6660 5.00e-04 AGGAgGaa
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6661 6.90e+03 CCaTGGTTTcCC
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6664 2.40e-01 GGAGttGAtT
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6665 5.90e+03 CAGCGG
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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 CAC0001

CAC0001 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
ATPase involved in DNA replication initiation cog/ cog
DNA replication origin binding go/ molecular_function
UDP-N-acetylglucosamine diphosphorylase activity go/ molecular_function
ATP binding go/ molecular_function
DNA-dependent DNA replication initiation go/ biological_process
regulation of DNA replication go/ biological_process
nucleoside-triphosphatase activity go/ molecular_function
DnaA tigr/ tigrfam
Module neighborhood information for CAC0001

CAC0001 has total of 45 gene neighbors in modules 3, 5
Gene neighbors (45)
Gene Common Name Description Module membership
CAC0001 dnaA DNA replication initiator protein, ATPase (NCBI ptt file) 3, 5
CAC0002 dnaN DNA polymerase III beta subunit (NCBI ptt file) 3, 283
CAC0224 CAC0224 Response regulator (CheY-like receiver domain and HTH DNA-binding domain) (NCBI ptt file) 3, 91
CAC0294 CAC0294 Magnesium and cobalt transporter (NCBI ptt file) 3, 5
CAC0978 CAC0978 Possible elongation subunit of DNA-dependent DNA polymerase (NCBI ptt file) 5, 268
CAC0988 CAC0988 Probably membrane protein (NCBI ptt file) 5, 134
CAC1195 ligA DNA ligase (NAD dependent), LigA (NCBI ptt file) 3, 5
CAC1241 radc RadC protein ortholog (NCBI ptt file) 3, 251
CAC1245 pbpA Penicillin-binding protein 2 (NCBI ptt file) 2, 5
CAC1279 hemN Coproporphyrinogen III oxidase (NCBI ptt file) 3, 106
CAC1306 CAC1306 Hypothetical protein (NCBI ptt file) 5, 51
CAC1309 CAC1309 Hypothetical protein (NCBI ptt file) 3, 51
CAC1495 CAC1495 Enzyme of dihydrofolate reductase family, ortholog YWFD B.subtilis (NCBI ptt file) 5, 247
CAC1685 CAC1685 Uncharacterized protein from YceG family (NCBI ptt file) 5, 315
CAC1687 CAC1687 Collagenase family protease (NCBI ptt file) 5, 315
CAC1716 CAC1716 Uncharacterized stress-induced protein, YicC family (NCBI ptt file) 3, 251
CAC1717 CAC1717 Uncharacterized conserved protein, YLOA ortholog (NCBI ptt file) 3, 91
CAC1718 CAC1718 Guanylate kinase, YLOD B.subtilis ortholog (NCBI ptt file) 3, 329
CAC1736 recG RecG helicase (NCBI ptt file) 3, 51
CAC1749 CAC1749 BioB/LipA-like protein (NCBI ptt file) 5, 283
CAC1793 lexA P-loop ATPase domain fused to LexA-like protein (NCBI ptt file) 3, 5
CAC1794 CAC1794 Predicted permease (NCBI ptt file) 3, 51
CAC1804 CAC1804 Exopolyphosphatase family protein (NCBI ptt file) 5, 213
CAC1806 CAC1806 Riboflavin kinase/FAD synthase (NCBI ptt file) 5, 213
CAC1818 CAC1818 Conserved membrane protein, possible 4-hydroxybenzoate octaprenyltranferase (NCBI ptt file) 3, 51
CAC2032 CAC2032 Hypothetical protein (NCBI ptt file) 3, 258
CAC2125 divIB Cell division septal protein divIB/FtsQ (NCBI ptt file) 2, 3
CAC2296 CAC2296 Uncharacterized protein, YigZ family (NCBI ptt file) 3, 91
CAC2297 CAC2297 Transcriptional regulator of MocR family (DNA-binding HTH domain and aminotransferase domain) (NCBI ptt file) 3, 91
CAC2323 CAC2323 Predicted membrane protein (NCBI ptt file) 5, 82
CAC2346 CAC2346 Glycosyltransferase (NCBI ptt file) 3, 100
CAC2550 CAC2550 Hypothetical protein (NCBI ptt file) 3, 258
CAC2672 CAC2672 Predicted membrane protein (NCBI ptt file) 5, 352
CAC2674 CAC2674 ATP-dependent superfamily I DNA helicase, PCRA (NCBI ptt file) 3, 98
CAC2698 CAC2698 Hypothetical protein (NCBI ptt file) 5, 351
CAC2770 CAC2770 Amino acid transporter (NCBI ptt file) 3, 51
CAC2844 galT Galactose-1-phosphate uridylyltransferase (NCBI ptt file) 5, 100
CAC2938 CAC2938 Hypothetical protein (NCBI ptt file) 5, 62
CAC3089 CAC3089 Hypothetical protein (NCBI ptt file) 3, 283
CAC3091 CAC3091 Fumarate hydratase, subunit A (N-terminal domain of FumA E.coli) class I (NCBI ptt file) 3, 13
CAC3151 rpmG L33 (NCBI ptt file) 5, 255
CAC3152 CAC3152 DNA-dependent RNA polymerase sigma subunit (NCBI ptt file) 5, 109
CAC3228 CAC3228 Predicted membrane protein (NCBI ptt file) 5, 117
CAC3308 CAC3308 Glycosyltransferase fused to TPR-repeat domain (NCBI ptt file) 3, 190
CAC3734 thdF Predicted GTPase, ThdF family (NCBI ptt file) 5, 100
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 CAC0001
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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