Organism : Clostridium acetobutylicum | Module List :
CAC3587

DNA replication protein DnaD (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
Putative primosome component and related proteins cog/ cog
DnaD_dom tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3587
(Mouseover regulator name to see its description)

CAC3587 is regulated by 18 influences and regulates 0 modules.
Regulators for CAC3587 (18)
Regulator Module Operator
CAC1046 287 tf
CAC1800 287 tf
CAC2473 287 tf
CAC2552 287 tf
CAC2568 287 tf
CAC3088 287 tf
CAC3507 287 tf
CAC3509 287 tf
CAC3611 287 tf
CAC0113 13 tf
CAC0174 13 tf
CAC0201 13 tf
CAC0723 13 tf
CAC1578 13 tf
CAC3406 13 tf
CAC3413 13 tf
CAC3424 13 tf
CAC3512 13 tf

Warning: CAC3587 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
6680 1.10e+01 GGaGggaTtA
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6681 1.10e+03 CgaGCgatAcc
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7226 2.00e-02 .aGGtG
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7227 4.00e+04 cGTAATTcACATAAAaGGTc
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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 CAC3587

CAC3587 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Putative primosome component and related proteins cog/ cog
DnaD_dom tigr/ tigrfam
Module neighborhood information for CAC3587

CAC3587 has total of 44 gene neighbors in modules 13, 287
Gene neighbors (44)
Gene Common Name Description Module membership
CAC0135 CAC0135 Hypothetical protein, CF-23 family (NCBI ptt file) 13, 247
CAC0237 CAC0237 ABC transporter, permease component (NCBI ptt file) 106, 287
CAC0248 CAC0248 Transposon related protein (NCBI ptt file) 13, 117
CAC0291 CAC0291 FUSION: methionine sintase I (cobalamin dependent) and 5,10 methylenetetrahydrofolate reductase (NCBI ptt file) 259, 287
CAC0325 CAC0325 Uncharacterized membrane protein, homolog of YtaF B.subtilis (NCBI ptt file) 13, 117
CAC0371 CAC0371 Response regulator (CheY-like domain and HTH domain) (NCBI ptt file) 71, 287
CAC0418 CAC0418 Predicted phosphatase, HAD family (NCBI ptt file) 261, 287
CAC0450 CAC0450 Response regulator (CheY-like and HTH domains) (NCBI ptt file) 13, 66
CAC0451 CAC0451 Sensory transduction histidine kinase (HAMP, HisKA, HATPase domains) (NCBI ptt file) 13, 140
CAC0589 birA Biotin-(acetyl-CoA carboxylase)ligase (NCBI ptt file) 13, 140
CAC0605 CAC0605 Predicted phosphatase (NCBI ptt file) 287, 356
CAC0607 CAC0607 Aspartyl aminopeptidase (NCBI ptt file) 287, 309
CAC0778 CAC0778 ATP-dependent RNA helicase, superfamily II (NCBI ptt file) 13, 66
CAC0820 CAC0820 Conserved protein, ortholog YwqG B.subtilis (NCBI ptt file) 13, 66
CAC1012 CAC1012 Uncharacterized membrane protein, homolog of YNGA/YWCD B.suntilis (NCBI ptt file) 13, 69
CAC1018 CAC1018 Predicted membrane protein (NCBI ptt file) 287, 326
CAC1046 CAC1046 Transcriptional regulator, LysR family (NCBI ptt file) 71, 287
CAC1330 CAC1330 Metal-dependent hydrolases of the beta-lactamase superfamily, possible sulfatase (NCBI ptt file) 287, 356
CAC1371 CAC1371 Possible kinase, diverged (NCBI ptt file) 13, 55
CAC1381 cbiJ/cobK precorrin-6x reductase (NCBI ptt file) 13, 55
CAC1424 CAC1424 Zn-dependent hydrolase, glyoxylase II family (NCBI ptt file) 287, 326
CAC1500 CAC1500 Predicted membrane protein (NCBI ptt file) 13, 351
CAC1516 CAC1516 Response regulator (CheY-like receiver domain and HTH DNA-binding domain) (NCBI ptt file) 140, 287
CAC1582 CAC1582 Membrane associated histidine kinase-like ATPase (NCBI ptt file) 259, 287
CAC1969 CAC1969 Possible plasmid transfer factor, TraK (NCBI ptt file) 287, 291
CAC2348 CAC2348 Glycosyltransferase (NCBI ptt file) 13, 312
CAC2349 CAC2349 Hypothetical protein (NCBI ptt file) 13, 100
CAC2453 CAC2453 CBS domain containing protein (NCBI ptt file) 13, 346
CAC2472 CAC2472 Alpha/beta superfamily hydrolase (NCBI ptt file) 261, 287
CAC2478 CAC2478 Predicted conserved membrane protein, possible homolog of CAAX-like membrane endopeptidase (NCBI ptt file) 13, 149
CAC2554 CAC2554 Hypothetical protein (NCBI ptt file) 13, 346
CAC2555 CAC2555 Hypothetical protein (NCBI ptt file) 13, 149
CAC2735 CAC2735 Response regulator (CheY-like receiver domain and HTH-type DNA-binding) (NCBI ptt file) 74, 287
CAC2907 CAC2907 Glycosyltransferase (NCBI ptt file) 13, 117
CAC2996 CAC2996 Superfamily II DNA/RNA helicase, SNF2 family (NCBI ptt file) 259, 287
CAC3088 CAC3088 NtrC family transcriptional regulator, ATPase domain fused to two PAS domains (NCBI ptt file) 113, 287
CAC3091 CAC3091 Fumarate hydratase, subunit A (N-terminal domain of FumA E.coli) class I (NCBI ptt file) 3, 13
CAC3240 CAC3240 Predicted membrane protein (NCBI ptt file) 13, 150
CAC3265 CAC3265 Predicted membrane protein (NCBI ptt file) 13, 99
CAC3457 CAC3457 Predicted membrane protein (NCBI ptt file) 287, 356
CAC3509 CAC3509 Transcriptional regulator, MerR family (duplicated domains) (NCBI ptt file) 287, 356
CAC3587 CAC3587 DNA replication protein DnaD (NCBI ptt file) 13, 287
CAC3596 pgsA Phosphatidylglycerophosphate synthase (NCBI ptt file) 13, 99
CAC3692 CAC3692 Hypothetical protein (NCBI ptt file) 13, 196
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 CAC3587
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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