Organism : Clostridium acetobutylicum | Module List :
CAC2990 csp

Cold shock protein (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Cold shock proteins cog/ cog
DNA binding go/ molecular_function
aspartate-semialdehyde dehydrogenase activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2990
(Mouseover regulator name to see its description)

CAC2990 is regulated by 19 influences and regulates 6 modules.
Regulators for CAC2990 csp (19)
Regulator Module Operator
CAC0144 76 tf
CAC0265 76 tf
CAC1536 76 tf
CAC1719 76 tf
CAC1941 76 tf
CAC2052 76 tf
CAC2113 76 tf
CAC3149 76 tf
CAC3199 76 tf
CAC3466 76 tf
CAC3731 76 tf
CAC0115 32 tf
CAC0254 32 tf
CAC0310 32 tf
CAC0493 32 tf
CAC0807 32 tf
CAC2222 32 tf
CAC2990 32 tf
CAC3037 32 tf

Warning: CAC2990 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
6718 3.20e-06 agGAGGTg
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6719 3.30e+00 GcAcaaAaa.actg
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6806 3.70e-01 agGAGg
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6807 6.50e+03 AAGGGgaGaAt
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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 CAC2990

CAC2990 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Cold shock proteins cog/ cog
DNA binding go/ molecular_function
aspartate-semialdehyde dehydrogenase activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for CAC2990

CAC2990 has total of 38 gene neighbors in modules 32, 76
Gene neighbors (38)
Gene Common Name Description Module membership
CAC0127 recR Recombination protein (recR) (NCBI ptt file) 32, 281
CAC0494 CAC0494 PemK family of DNA-binding proteins (NCBI ptt file) 32, 232
CAC0827 CAC0827 Fructose-bisphosphate aldolase (NCBI ptt file) 32, 295
CAC1015 CAC1015 Pseudouridylate synthase (NCBI ptt file) 76, 306
CAC1234 pheB Chorismate mutase PheB of B.subtilis ortholog (NCBI ptt file) 76, 215
CAC1251 rodA Cell division protein, rodA/ftsW/spoVE family (NCBI ptt file) 76, 281
CAC1258 CAC1258 Hypothetical protein (NCBI ptt file) 32, 61
CAC1259 rpl27 Ribosomal protein L27 (NCBI ptt file) 32, 61
CAC1289 CAC1289 Uncharacterized conserved protein, YqeY B.subtilis ortholog (NCBI ptt file) 32, 232
CAC1501 CAC1501 DNA-methyltransferase (cytosine-specific), ortholog of BSP6I Bsubtilis (NCBI ptt file) 76, 79
CAC1612 CAC1612 Probable cation efflux pump, multidrug resistance protein (FS) (NCBI ptt file) 76, 149
CAC1613 CAC1613 ABC-type multidrug/protein/lipid transport system, membrane ATPase component (NCBI ptt file) 76, 249
CAC1745 rpmF Ribosomal protein L32 (NCBI ptt file) 32, 232
CAC1747 acpA Acyl carrier protein, ACP (NCBI ptt file) 32, 232
CAC1757 CAC1757 RimM protein, required for 16S rRNA processing (NCBI ptt file) 76, 297
CAC1758 trmD TRNA-(guanine-N1)-methyltransferase, TrmD (NCBI ptt file) 76, 297
CAC1759 rplS Ribosomal protein L19 (NCBI ptt file) 32, 237
CAC2062 CAC2062 TRNA nucleotidyltransferase family enzyme (NCBI ptt file) 76, 211
CAC2228 CAC2228 Hypothetical protein (NCBI ptt file) 76, 281
CAC2339 CAC2339 Uncharacterized protein, YBBK B.subtilis ortholog (NCBI ptt file) 76, 123
CAC2359 rplT Ribosomal protein L20 (NCBI ptt file) 32, 61
CAC2360 rpmL Ribosomal protein L35 (NCBI ptt file) 32, 61
CAC2361 infC Translation initiation factor IF3 (NCBI ptt file) 32, 61
CAC2373 CAC2373 Predicted membrane protein (NCBI ptt file) 76, 84
CAC2713 CAC2713 AT-rich DNA-binding protein (NCBI ptt file) 76, 281
CAC2852 comFC Predicted amidophosphoribosyltransferase, ComFC B.suntilis ortholog (NCBI ptt file) 76, 149
CAC2855 CAC2855 Predicted membrane protein (NCBI ptt file) 59, 76
CAC2856 metK S-adenosylmethionine synthetase (NCBI ptt file) 32, 232
CAC2872 CAC2872 Predicted membrane protein in FoF1-type ATP synthase operon (NCBI ptt file) 76, 162
CAC2881 CAC2881 Protein-tyrosine-phosphatase, YWLE B.subtilis ortholog (NCBI ptt file) 35, 76
CAC2990 csp Cold shock protein (NCBI ptt file) 32, 76
CAC3200 CAC3200 Predicted transcriptional regulator, homolog of Bvg accessory factor (NCBI ptt file) 76, 116
CAC3211 hbs DNA binding protein HU (NCBI ptt file) 32, 295
CAC3537 CAC3537 Fragment of SECA (fragment) (NCBI ptt file) 76, 229
CAC3568 accA Acetyl-CoA carboxylase alpha subunit (NCBI ptt file) 32, 206
CAC3722 rpsR Ribosomal protein S18 (NCBI ptt file) 32, 61
CAC3723 ssb Single strand DNA binding protein, SSB (NCBI ptt file) 32, 61
CAC3724 rpsF Ribosomal protein S6 (NCBI ptt file) 32, 61
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 CAC2990
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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