Organism : Clostridium acetobutylicum | Module List :
CAC3488

Predicted transcriptional regulator (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
Predicted transcriptional regulators cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3488
(Mouseover regulator name to see its description)

CAC3488 is regulated by 15 influences and regulates 12 modules.
Regulators for CAC3488 (15)
Regulator Module Operator
CAC0723 69 tf
CAC0859 69 tf
CAC1046 69 tf
CAC1670 69 tf
CAC2990 69 tf
CAC3406 69 tf
CAC3488 69 tf
CAC3494 69 tf
CAC3512 69 tf
CAC3651 69 tf
CAC1463 208 tf
CAC2568 208 tf
CAC2768 208 tf
CAC3433 208 tf
CAC3488 208 tf
Regulated by CAC3488 (12)
Module Residual Genes
24 0.32 20
69 0.46 29
102 0.55 24
123 0.59 24
150 0.40 31
169 0.40 24
190 0.46 30
202 0.35 20
208 0.39 26
306 0.38 20
312 0.61 34
336 0.38 26
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
6792 8.00e-01 cgAAagAGtttcaAa.g.T.atgc
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6793 2.80e+01 AGGaGtG
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7068 8.80e-06 TaAaGGaG
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7069 2.00e+03 TtGCaccAGC
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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 CAC3488

CAC3488 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted transcriptional regulators cog/ cog
Module neighborhood information for CAC3488

CAC3488 has total of 54 gene neighbors in modules 69, 208
Gene neighbors (54)
Gene Common Name Description Module membership
CAC0041 CAC0041 Uncharacterized small conserved protein, homolog of yfjA/yukE B.subtilis (NCBI ptt file) 208, 264
CAC0075 CAC0075 Ferredoxin (NCBI ptt file) 69, 150
CAC0136 CAC0136 Hypothetical protein (NCBI ptt file) 69, 205
CAC0137 CAC0137 Hypothetical protein, CF-5 family (NCBI ptt file) 69, 205
CAC0227 CAC0227 Predicted permease (NCBI ptt file) 169, 208
CAC0501 bacA Bacitracin resistance protein (bacA) (NCBI ptt file) 69, 300
CAC0859 CAC0859 Ortholog putative anti-SigV factor [Bacillus subtilis] (NCBI ptt file) 69, 344
CAC1012 CAC1012 Uncharacterized membrane protein, homolog of YNGA/YWCD B.suntilis (NCBI ptt file) 13, 69
CAC1094 CAC1094 Cation efflux system protein (NCBI ptt file) 208, 320
CAC1247 pbpA Penicillin-binding protein 2 (NCBI ptt file) 144, 208
CAC1387 CAC1387 Membrane associated chemotaxis sensory transducer protein (MSP domain and HAMP domain) (NCBI ptt file) 100, 208
CAC1399 CAC1399 ABC transporter, permease component (NCBI ptt file) 69, 306
CAC1513 asrA Anaerobic sulfite reductase (Fe-S subunit) (NCBI ptt file) 208, 240
CAC1521 CAC1521 Uncharacterized membrane protein, yetF/ydfS/ykjA/yrbG/ydfR B.subtilis ortholog (NCBI ptt file) 150, 208
CAC1555 CAC1555 Flagellin (NCBI ptt file) 53, 69
CAC1592 CAC1592 Predicted permease, YCGR B.subtilis ortholog (NCBI ptt file) 69, 345
CAC1593 CAC1593 Zn-binding lipoprotein related (surface adhesin A), ADHS (NCBI ptt file) 69, 282
CAC1614 CAC1614 Predicted glycosyltransferase (NCBI ptt file) 69, 117
CAC1615 CAC1615 Predicted glycosyltransferase (NCBI ptt file) 69, 82
CAC1645 CAC1645 Ankyrin repeats containing protein (NCBI ptt file) 69, 102
CAC1702 CAC1702 Hypothetical protein (NCBI ptt file) 208, 336
CAC1959 CAC1959 Uncharacterized protein, YYAC B.subtilis homolog (fragment) (NCBI ptt file) 190, 208
CAC1960 CAC1960 Uncharacterized protein, YYAC B.subtilis homolog (NCBI ptt file) 208, 336
CAC1963 CAC1963 5'-nucleotidase/2',3'-cyclic phosphodiesterase related enzyme (NCBI ptt file) 69, 205
CAC1974 CAC1974 Hypothetical secreted protein (NCBI ptt file) 208, 336
CAC1981 CAC1981 Hypothetical protein (NCBI ptt file) 208, 336
CAC1995 CAC1995 Hypothetical protein (NCBI ptt file) 69, 166
CAC2028 CAC2028 Hypothetical protein, CF-4 family (NCBI ptt file) 205, 208
CAC2046 CAC2046 Predicted membrane protein (NCBI ptt file) 208, 336
CAC2048 CAC2048 Uncharacterized secreted protein (NCBI ptt file) 208, 336
CAC2049 CAC2049 Predicted membrane protein (NCBI ptt file) 208, 336
CAC2096 CAC2096 Hypothetical protein (NCBI ptt file) 69, 312
CAC2177 CAC2177 Ucharacterized protein, CGEB homolog (NCBI ptt file) 69, 361
CAC2257 CAC2257 Hypothetical protein (NCBI ptt file) 4, 69
CAC2400 CAC2400 Serine/threonine kinase related protein, inactivated (HRDL motif absent) (fragment) (NCBI ptt file) 69, 137
CAC2402 CAC2402 TPR repeats containing protein (NCBI ptt file) 69, 102
CAC2419 CAC2419 Methyl-accepting chemotaxis protein (NCBI ptt file) 69, 205
CAC2493 CAC2493 Phospholipase C family protein (NCBI ptt file) 205, 208
CAC2503 CAC2503 Hypothetical protein (NCBI ptt file) 65, 208
CAC2560 CAC2560 Predicted acetyltransferase (NCBI ptt file) 69, 190
CAC2732 CAC2732 ABC transporter, ATPase component (NCBI ptt file) 69, 359
CAC2733 CAC2733 Uncharacterized conserved membrane protein (NCBI ptt file) 69, 74
CAC2745 CAC2745 Membrane associated methyl-accepting chemotaxis protein (NCBI ptt file) 208, 236
CAC2877 CAC2877 ABC-type iron (III) transport system, ATPase component (NCBI ptt file) 69, 344
CAC2878 CAC2878 ABC-type iron (III) transport system, permease component (NCBI ptt file) 69, 322
CAC2921 thiH Thiamine biosynthesis enzyme, thiH (NCBI ptt file) 208, 363
CAC2923 CAC2923 Dinucleotide-utilizing enzyme involved in molybdopterin/thiamine biosynthesis (NCBI ptt file) 208, 363
CAC2924 thiS Uncharacterized protein, possibly involved in thiamine biosynthesis (NCBI ptt file) 208, 336
CAC3385 CAC3385 Hypothetical protein (NCBI ptt file) 69, 205
CAC3415 CAC3415 ABC-type multidrug/protein/lipid transport system, ATPase component (NCBI ptt file) 123, 208
CAC3476 CAC3476 Methyl-accepting chemotaxis protein (NCBI ptt file) 208, 353
CAC3488 CAC3488 Predicted transcriptional regulator (NCBI ptt file) 69, 208
CAC3489 CAC3489 Hypothetical protein (NCBI ptt file) 69, 74
CAC3554 CAC3554 Siderophore/Surfactin synthetase related protein (NCBI ptt file) 26, 208
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 CAC3488
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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