Organism : Synechococcus elongatus PCC 7942 | Module List :
Synpcc7942_1016

CheW protein (IMGterm)

CircVis
Functional Annotations (6)
Function System
Chemotaxis signal transduction protein cog/ cog
signal transducer activity go/ molecular_function
intracellular go/ cellular_component
chemotaxis go/ biological_process
signal transduction go/ biological_process
Two-component system kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Synpcc7942_1016
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Synpcc7942_1016!

Warning: Synpcc7942_1016 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 6 motifs predicted.

Motif Table (6)
Motif Id e-value Consensus Motif Logo
1550 1.30e+03 gGc.tcgCTAggcTgAA
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1551 1.20e+04 tagc.aT..tTa.agaAAaaTagt
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1552 1.20e+04 AAActcTtcaaAaA
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2060 5.90e+00 tccCGAtCgcttgg
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2061 3.70e+02 taGtcTAaGcttAAaTtCTa
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2062 6.70e+03 tTTGgtgCTG
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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 Synpcc7942_1016

Synpcc7942_1016 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Chemotaxis signal transduction protein cog/ cog
signal transducer activity go/ molecular_function
intracellular go/ cellular_component
chemotaxis go/ biological_process
signal transduction go/ biological_process
Two-component system kegg/ kegg pathway
Module neighborhood information for Synpcc7942_1016

Synpcc7942_1016 has total of 52 gene neighbors in modules 10, 181
Gene neighbors (52)
Gene Common Name Description Module membership
Synpcc7942_0012 rpsF SSU ribosomal protein S6P (IMGterm) 122, 181
Synpcc7942_0079 conserved hypothetical protein YCF41 10, 181
Synpcc7942_0139 "acetolactate synthase, large subunit (EC 2.2.1.6) (IMGterm)" 38, 181
Synpcc7942_0140 hypothetical protein 10, 16
Synpcc7942_0164 Iojap-related protein 122, 181
Synpcc7942_0217 phosphatase-like 9, 10
Synpcc7942_0233 hypothetical protein 2, 10
Synpcc7942_0267 gidB 16S rRNA m(7)G-527 methyltransferase (EC 2.1.1.-) (IMGterm) 10, 49
Synpcc7942_0289 secA protein translocase subunit secA (IMGterm) 181, 198
Synpcc7942_0301 single-strand binding protein (IMGterm) 107, 181
Synpcc7942_0343 photosystem II 11 kD protein 112, 181
Synpcc7942_0361 hypothetical protein 10, 55
Synpcc7942_0410 hypothetical protein 38, 181
Synpcc7942_0430 1-deoxy-D-xylulose-5-phosphate synthase (EC 2.2.1.7) (IMGterm) 112, 181
Synpcc7942_0468 secG "preprotein translocase, SecG subunit" 112, 181
Synpcc7942_0514 hypothetical protein 5, 181
Synpcc7942_0549 hypothetical protein 181, 198
Synpcc7942_0723 hypothetical protein 10, 82
Synpcc7942_0728 hypothetical protein 107, 181
Synpcc7942_0762 hypothetical protein 10, 21
Synpcc7942_0774 esterase (EC:4.2.99.20) 10, 205
Synpcc7942_0900 hypothetical protein 10, 205
Synpcc7942_0916 hypothetical protein 10, 122
Synpcc7942_0956 hypothetical protein 181, 198
Synpcc7942_1016 CheW protein (IMGterm) 10, 181
Synpcc7942_1127 microcin-processing peptidase 2. Unknown type peptidase. MEROPS family U62 (IMGterm) 122, 181
Synpcc7942_1180 NADH dehydrogenase subunit A (EC 1.6.5.3) (IMGterm) 43, 181
Synpcc7942_1181 NADH dehydrogenase subunit B (EC 1.6.5.3) (IMGterm) 43, 181
Synpcc7942_1182 NADH dehydrogenase subunit C (EC 1.6.5.3) (IMGterm) 43, 181
Synpcc7942_1294 serine/threonine protein kinase (IMGterm) 10, 21
Synpcc7942_1314 membrane protease FtsH catalytic subunit (EC 3.4.24.-) (IMGterm) 10, 49
Synpcc7942_1352 acetyl-coenzyme A synthetase (EC 6.2.1.1) (IMGterm) 10, 112
Synpcc7942_1374 ribosomal large subunit pseudouridine synthase D (EC:5.4.99.12) 10, 205
Synpcc7942_1400 "Endo-1,4-beta-xylanase (EC:3.2.1.8)" 10, 50
Synpcc7942_1515 protein serine/threonine phosphatase (IMGterm) 10, 45
Synpcc7942_1675 hypothetical protein 10, 21
Synpcc7942_1710 RNA polymerase subunit omega (rpoZ) (EC:2.7.7.6) 122, 181
Synpcc7942_1750 conserved hypothetical protein YCF35 52, 181
Synpcc7942_1751 hypothetical protein 52, 181
Synpcc7942_1845 hypothetical protein 10, 21
Synpcc7942_1860 "two component transcriptional regulator, LuxR family (IMGterm)" 8, 181
Synpcc7942_1882 probable photosystem II 12 kD extrinsic protein 112, 181
Synpcc7942_1980 "transcriptional regulator, LysR family (IMGterm)" 10, 45
Synpcc7942_2046 glycine cleavage system H protein 84, 181
Synpcc7942_2096 diguanylate cyclase with GAF sensor (IMGterm) 10, 205
Synpcc7942_2178 hypothetical protein 10, 21
Synpcc7942_2264 "transcriptional regulator, LuxR family (IMGterm)" 82, 181
Synpcc7942_2321 TPR repeat 82, 181
Synpcc7942_2322 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C (EC 6.3.5.-) (IMGterm) 82, 181
Synpcc7942_2349 twitching motility protein 10, 49
Synpcc7942_2540 blue-copper-protein-like protein 10, 205
Synpcc7942_2547 hypothetical protein 10, 49
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 Synpcc7942_1016
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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