Organism : Clostridium acetobutylicum | Module List :
CAC2616

Predicted 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 CAC2616
(Mouseover regulator name to see its description)

CAC2616 is regulated by 18 influences and regulates 22 modules.
Regulators for CAC2616 (18)
Regulator Module Operator
CAC0863 290 tf
CAC1046 290 tf
CAC1430 290 tf
CAC2616 290 tf
CAC2794 290 tf
CAC2859 290 tf
CAC3214 290 tf
CAC3438 290 tf
CAC0474 135 tf
CAC0627 135 tf
CAC1430 135 tf
CAC2074 135 tf
CAC2546 135 tf
CAC2616 135 tf
CAC2859 135 tf
CAC3214 135 tf
CAC3406 135 tf
CAC3487 135 tf

Warning: CAC2616 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
6922 3.90e-09 aGGAGG
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6923 7.60e+03 CCGacC
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7232 3.50e-08 tGGaGG
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7233 1.00e+03 gcTGCC
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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 CAC2616

CAC2616 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 CAC2616

CAC2616 has total of 27 gene neighbors in modules 135, 290
Gene neighbors (27)
Gene Common Name Description Module membership
CAC0276 CAC0276 Uncharacterized possible metal-binding protein (NCBI ptt file) 45, 135
CAC0283 CAC0283 Molybdopterin biosynthesis protein (NCBI ptt file) 95, 290
CAC0469 spmA Spore maturation protein A (gene spmA) (NCBI ptt file) 15, 290
CAC0562 CAC0562 Predicted membrane protein (NCBI ptt file) 135, 197
CAC0563 CAC0563 Predicted membrane protein (NCBI ptt file) 135, 197
CAC0623 CAC0623 Hypothetical protein (NCBI ptt file) 135, 308
CAC0737 CAC0737 NADP-specific glutamate dehydrogenase (NCBI ptt file) 45, 290
CAC0808 hybG Hydrogenase expression factor (hybG) (NCBI ptt file) 95, 290
CAC0809 hypE Hydrogenase formation factor (hypE) (NCBI ptt file) 95, 290
CAC1236 CAC1236 Hypothetical protein (NCBI ptt file) 45, 135
CAC1487 CAC1487 Uncharacterized protein, similar to TlpA of B.subtilis (NCBI ptt file) 45, 135
CAC1673 gltA Large subunit of NADH-dependent glutamate synthase (NCBI ptt file) 263, 290
CAC1713 CAC1713 Coat morphogenesis sporulation protein spoIVA (NCBI ptt file) 188, 290
CAC1864 CAC1864 Hypothetical protein (NCBI ptt file) 203, 290
CAC2059 CAC2059 Uncharacterized protein, YTFJ Bacillus subtilis ortholog (NCBI ptt file) 135, 290
CAC2342 CAC2342 Predicted membrane protein (NCBI ptt file) 135, 308
CAC2384 CAC2384 Hypothetical protein (NCBI ptt file) 135, 197
CAC2615 CAC2615 Uncharacterized conserved protein, CotF B.subtilis family (NCBI ptt file) 135, 203
CAC2616 CAC2616 Predicted iron-dependent transcription repressor (NCBI ptt file) 135, 290
CAC2728 CAC2728 Hypothetical protein, CF-30 family (NCBI ptt file) 135, 308
CAC2861 spoIID Sporulation protein SpoIID (NCBI ptt file) 263, 290
CAC2905 CAC2905 Uncharacterized protein, YABG B.subtilis ortholog (NCBI ptt file) 135, 308
CAC2984 CAC2984 Hypothetical protein (NCBI ptt file) 188, 290
CAC3081 CAC3081 Spore-cortex-lytic enzyme, SLEB (NCBI ptt file) 203, 290
CAC3214 CAC3214 Stage V sporulation protein T, AbrB family transcriptional regulator (NCBI ptt file) 45, 135
CAC3244 CAC3244 Spore cortex-lytic enzyme, pre-pro-form (diverged form of N-acetylmuramyl-L-alanine amidase); peptidoglycan-binding domain (NCBI ptt file) 135, 308
CAC3540 CAC3540 Hypothetical protein (NCBI ptt file) 45, 135
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 CAC2616
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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