Organism : Synechococcus elongatus PCC 7942 | Module List :
Synpcc7942_0763

"transcriptional regulator, XRE family (IMGterm)"

CircVis
Functional Annotations (2)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Synpcc7942_0763
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Synpcc7942_0763!

Warning: Synpcc7942_0763 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
2054 2.90e-03 TtGtcagTccTC.agAgtTt
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2055 3.40e+00 CAAAAAttcTGaATtctctg
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2056 3.50e+02 agaGCcattCAg..CatgacG
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2078 4.20e+00 AT.GgCt.Agcc.ggggAac.
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2079 2.90e+04 AAcTgCaGAA
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2080 3.60e+04 CCGaTCAGgtTCA
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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_0763

Synpcc7942_0763 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for Synpcc7942_0763

Synpcc7942_0763 has total of 56 gene neighbors in modules 179, 187
Gene neighbors (56)
Gene Common Name Description Module membership
Synpcc7942_0131 cyclic nucleotide-binding domain (cNMP-BD) protein 41, 187
Synpcc7942_0135 Methylase involved in ubiquinone/menaquinone biosynthesis-like (EC:2.1.1.-) 126, 179
Synpcc7942_0154 hypothetical protein 179, 187
Synpcc7942_0292 Phosphopantothenate-cysteine ligase (EC 6.3.2.5) / Phosphopantothenoylcysteine decarboxylase (EC 4.1.1.36) (IMGterm) 19, 187
Synpcc7942_0339 hypothetical protein 118, 179
Synpcc7942_0340 hypothetical protein 118, 179
Synpcc7942_0373 hypothetical protein 102, 179
Synpcc7942_0498 "mannose-1-phosphate guanyltransferase (EC:5.4.2.8, EC:2.7.7.13)" 121, 179
Synpcc7942_0566 HAD-superfamily hydrolase subfamily IIB 179, 187
Synpcc7942_0568 cytosine deaminase (EC:3.5.4.1) 7, 179
Synpcc7942_0671 hypothetical protein 120, 179
Synpcc7942_0692 hypothetical protein 4, 179
Synpcc7942_0741 Phage tail protein I 69, 187
Synpcc7942_0756 "chain A, D20c mutant of T4 lysozyme (EC:3.2.1.17)" 179, 187
Synpcc7942_0763 "transcriptional regulator, XRE family (IMGterm)" 179, 187
Synpcc7942_0784 hypothetical protein 19, 179
Synpcc7942_0791 polyA polymerase (EC:2.7.7.19) 64, 179
Synpcc7942_0937 hypothetical protein (EC:3.1.2.6) 80, 187
Synpcc7942_0958 purN formyltetrahydrofolate-dependent phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) (IMGterm) 179, 187
Synpcc7942_0961 cell envelope-related function transcriptional attenuator common domain 64, 187
Synpcc7942_0981 hypothetical protein 15, 187
Synpcc7942_1019 4-alpha-glucanotransferase (IMGterm) 121, 179
Synpcc7942_1020 O-succinylbenzoate-CoA synthase-like (EC:4.2.1.113) 69, 179
Synpcc7942_1034 Transglutaminase-like 15, 187
Synpcc7942_1044 thymidylate synthase (FAD) (EC 2.1.1.148) (IMGterm) 179, 187
Synpcc7942_1070 oxidoreductase aldo/keto reductase 187, 192
Synpcc7942_1097 hypothetical protein 123, 187
Synpcc7942_1155 hypothetical protein 123, 179
Synpcc7942_1172 lnt apolipoprotein N-acyltransferase (EC:2.3.1.-) 17, 187
Synpcc7942_1218 circadian clock protein KaiA 31, 179
Synpcc7942_1222 truB tRNA pseudouridine synthase B (EC 4.2.1.70) (IMGterm) 28, 179
Synpcc7942_1223 DevC protein 13, 187
Synpcc7942_1242 "transcriptional regulator, LysR family (IMGterm)" 41, 179
Synpcc7942_1260 hypothetical protein 4, 179
Synpcc7942_1288 hypothetical protein 18, 187
Synpcc7942_1301 ATP-dependent DNA helicase RecQ (EC 3.6.1.-) (IMGterm) 179, 187
Synpcc7942_1311 hypothetical protein 4, 187
Synpcc7942_1328 hypothetical protein 22, 187
Synpcc7942_1332 hypothetical protein 140, 187
Synpcc7942_1333 preQ(0) biosynthesis protein QueC (IMGterm) 17, 187
Synpcc7942_1334 "aminodeoxychorismate synthase, subunit I (EC 6.3.5.8) (IMGterm)" 17, 187
Synpcc7942_1335 probable branched-chain amino acid aminotransferase (EC:2.6.1.42) 17, 187
Synpcc7942_1371 magnesium and cobalt transport protein CorA 15, 179
Synpcc7942_1372 methionine synthase (B12-dependent) (EC 2.1.1.13) (IMGterm) 32, 179
Synpcc7942_1696 hypothetical protein 11, 179
Synpcc7942_1725 "transcriptional regulator, GntR family (IMGterm)" 179, 187
Synpcc7942_1767 cytochrome bd plastoquinol oxidase subunit 1 apoprotein (EC 1.10.3.-) (IMGterm) 92, 179
Synpcc7942_1769 hypothetical protein 95, 179
Synpcc7942_1918 UDP-glucose:tetrahydrobiopterin glucosyltransferase (EC:2.4.1.-) 179, 187
Synpcc7942_1985 hypothetical protein 117, 179
Synpcc7942_2150 penicillin amidase (EC 3.5.1.11). Cysteine peptidase. MEROPS family C59 (IMGterm) 19, 187
Synpcc7942_2278 hypothetical protein 179, 187
Synpcc7942_2394 "sodium/proton antiporter, CPA1 family (TC 2.A.36) (IMGterm)" 64, 179
Synpcc7942_2404 hypothetical protein 13, 179
Synpcc7942_2462 probable sugar kinase (EC:2.7.1.17) 18, 179
Synpcc7942_2464 N-acylglucosamine-6-phosphate 2-epimerase (EC:5.1.3.9) 124, 179
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_0763
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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