Organism : Clostridium acetobutylicum | Module List :
CAC1989

ABC-type iron (III) transport system, ATPase component (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components cog/ cog
ATP binding go/ molecular_function
iron-chelate-transporting ATPase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1989
(Mouseover regulator name to see its description)

CAC1989 is regulated by 27 influences and regulates 0 modules.
Regulators for CAC1989 (27)
Regulator Module Operator
CAC0310 294 tf
CAC0841 294 tf
CAC1264 294 tf
CAC1481 294 tf
CAC1668 294 tf
CAC2071 294 tf
CAC2552 294 tf
CAC3142 294 tf
CAC3149 294 tf
CAC3673 294 tf
CAC0681 68 tf
CAC0693 68 tf
CAC0768 68 tf
CAC0841 68 tf
CAC1689 68 tf
CAC1698 68 tf
CAC1753 68 tf
CAC1770 68 tf
CAC1867 68 tf
CAC2052 68 tf
CAC2476 68 tf
CAC3063 68 tf
CAC3143 68 tf
CAC3149 68 tf
CAC3409 68 tf
CAC3485 68 tf
CAC3603 68 tf

Warning: CAC1989 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
6790 3.10e+03 CcCCGT
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6791 3.90e+03 GTGAGGTG
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7240 9.70e+00 AGGtGc
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7241 3.00e+03 GCaGGGc
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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 CAC1989

CAC1989 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components cog/ cog
ATP binding go/ molecular_function
iron-chelate-transporting ATPase activity go/ molecular_function
Module neighborhood information for CAC1989

CAC1989 has total of 43 gene neighbors in modules 68, 294
Gene neighbors (43)
Gene Common Name Description Module membership
CAC0186 CAC0186 Xre family DNA-binding domain and TPR-repeat-containing protein (NCBI ptt file) 68, 183
CAC0653 CAC0653 Response regulator (CheY-like receiver domain and HTH DNA binding domain) (NCBI ptt file) 294, 317
CAC0654 CAC0654 Sensory transduction histidine kinase (NCBI ptt file) 294, 317
CAC0985 CAC0985 ABC transporter, permease component (NCBI ptt file) 146, 294
CAC1034 CAC1034 Hypothetical protein (NCBI ptt file) 73, 294
CAC1147 CAC1147 Hypothetical protein (NCBI ptt file) 16, 68
CAC1148 CAC1148 Hypothetical protein (NCBI ptt file) 16, 68
CAC1151 CAC1151 Hypothetical protein (NCBI ptt file) 16, 68
CAC1154 CAC1154 Hypothetical protein (NCBI ptt file) 16, 68
CAC1220 CAC1220 Hypothetical protein (NCBI ptt file) 68, 275
CAC1450 CAC1450 Predicted alpha/beta superfamily hydrolase (NCBI ptt file) 294, 345
CAC1533 CAC1533 Hypothetical protein (NCBI ptt file) 68, 336
CAC1770 CAC1770 RNA polymerase sigma factor, SigK-like (NCBI ptt file) 53, 68
CAC1986 CAC1986 Hypothetical protein (NCBI ptt file) 68, 183
CAC1988 CAC1988 Ferrichrome-binding periplasmic protein (NCBI ptt file) 68, 97
CAC1989 CAC1989 ABC-type iron (III) transport system, ATPase component (NCBI ptt file) 68, 294
CAC1990 CAC1990 ABC-type iron (III) transport system, permease component (NCBI ptt file) 166, 294
CAC1991 CAC1991 Uncharacterized protein, YIIM family (NCBI ptt file) 68, 294
CAC1992 moaC Molybdenum cofactor biosynthesis enzyme, MoaC (NCBI ptt file) 68, 166
CAC1993 moaA Molybdenum cofactor biosynthesis enzyme MoaA, Fe-S oxidoreductase (NCBI ptt file) 97, 294
CAC1994 moaB Molybdopterin biosynthesis enzyme, MoaB (NCBI ptt file) 53, 68
CAC1996 CAC1996 Hypothetical protein (NCBI ptt file) 68, 97
CAC1997 CAC1997 Predicted glycosyltransferase (NCBI ptt file) 68, 97
CAC1998 CAC1998 ABC-type transport system, ATPase component (NCBI ptt file) 68, 97
CAC1999 CAC1999 Uncharacterized protein related to hypothetical protein Cj1507c from Campylobacter jejuni (NCBI ptt file) 97, 294
CAC2000 iorB Indolepyruvate ferredoxin oxidoreductase, subunit beta (NCBI ptt file) 68, 294
CAC2002 CAC2002 Predicted iron-sulfur flavoprotein (NCBI ptt file) 68, 97
CAC2006 CAC2006 Enzyme of siderophore/surfactin biosynthesis (NCBI ptt file) 68, 97
CAC2008 pksF 3-oxoacyl-(acyl-carrier-protein) synthase (NCBI ptt file) 68, 97
CAC2012 fadB Enoyl-CoA hydratase (NCBI ptt file) 97, 294
CAC2310 CAC2310 Methenyl tetrahydrofolate cyclohydrolase (serine cycle enzyme) (NCBI ptt file) 57, 294
CAC2336 CAC2336 TPR repeats containing protein (NCBI ptt file) 53, 294
CAC2337 CAC2337 Phosphomannomutase (NCBI ptt file) 225, 294
CAC2403 CAC2403 Predicted membrane protein (NCBI ptt file) 68, 115
CAC2481 CAC2481 Predicted kinase from adenilate kinase family, FLAR-like protein (NCBI ptt file) 146, 294
CAC2492 CAC2492 Predicted membrane, YNAG B.subtilis ortholog (NCBI ptt file) 270, 294
CAC2571 CAC2571 Predicted acetyltransferase (NCBI ptt file) 67, 294
CAC3303 CAC3303 Superfamily II DNA/RNA helicases, SNF2 family (NCBI ptt file) 71, 294
CAC3479 CAC3479 Hypothetical protein (NCBI ptt file) 26, 68
CAC3573 fabF 3-oxoacyl-(acyl-carrier-protein) synthase I (NCBI ptt file) 68, 183
CAC3628 oppF Oligopeptide ABC transporter, ATPase component (NCBI ptt file) 270, 294
CAC3629 oppD Oligopeptide ABC transporter, ATPase component (NCBI ptt file) 270, 294
CAC3693 CAC3693 Predicted membrane protein (NCBI ptt file) 146, 294
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.
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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.

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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.

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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.

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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
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Comments for CAC1989
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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