Organism : Synechococcus elongatus PCC 7942 | Module List :
Synpcc7942_1521

Sec-independent protein translocase TatD (EC 3.1.21.-) (IMGterm)

CircVis
Functional Annotations (2)
Function System
Mg-dependent DNase cog/ cog
TIGR00010 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Synpcc7942_1521
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Synpcc7942_1521!

Warning: Synpcc7942_1521 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
1649 3.90e+00 AGcCaATcgccgcAa
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1650 1.50e+00 tgcTGAAaccGctg.AGAa
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1651 3.30e+03 gttGCtgcAatgcctaAgcttttg
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1760 1.50e+02 aAgAGCtGa.tGAtt
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1761 9.00e+03 TtTtATtCaAtT
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1762 5.10e+03 TcTGATTGcTG
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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_1521

Synpcc7942_1521 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Mg-dependent DNase cog/ cog
TIGR00010 tigr/ tigrfam
Module neighborhood information for Synpcc7942_1521

Synpcc7942_1521 has total of 51 gene neighbors in modules 43, 80
Gene neighbors (51)
Gene Common Name Description Module membership
Synpcc7942_0082 ATPase 80, 97
Synpcc7942_0127 "transcriptional regulator, Crp/Fnr family (IMGterm)" 80, 161
Synpcc7942_0165 hypothetical protein 11, 43
Synpcc7942_0166 asparaginase (EC 3.5.1.1) (IMGterm) 43, 122
Synpcc7942_0297 membrane protease FtsH catalytic subunit (EC 3.4.24.-) (IMGterm) 43, 84
Synpcc7942_0694 SSU ribosomal protein S1P (IMGterm) 43, 200
Synpcc7942_0937 hypothetical protein (EC:3.1.2.6) 80, 187
Synpcc7942_0942 membrane protease FtsH catalytic subunit (EC 3.4.24.-) (IMGterm) 43, 84
Synpcc7942_1036 hypothetical protein 41, 80
Synpcc7942_1085 glycogen branching enzyme (EC 2.4.1.18) (IMGterm) 31, 43
Synpcc7942_1178 photosystem II stability/assembly factor 43, 163
Synpcc7942_1179 rubredoxin 43, 163
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_1184 6-pyruvoyl-tetrahydropterin synthase-like protein (EC:4.2.3.12) 43, 135
Synpcc7942_1216 circadian clock protein KaiC (IMGterm) 31, 80
Synpcc7942_1217 circadian clock protein KaiB 31, 80
Synpcc7942_1241 nitrite reductase related protein 80, 94
Synpcc7942_1485 hypothetical protein 80, 160
Synpcc7942_1497 hypothetical protein 43, 140
Synpcc7942_1520 rpsT SSU ribosomal protein S20P (IMGterm) 31, 80
Synpcc7942_1521 Sec-independent protein translocase TatD (EC 3.1.21.-) (IMGterm) 43, 80
Synpcc7942_1522 rpoB DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) (IMGterm) 19, 43
Synpcc7942_1523 DNA-directed RNA polymerase gamma chain (EC 2.7.7.6) (IMGterm) 19, 43
Synpcc7942_1524 DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) (IMGterm) 5, 43
Synpcc7942_1561 hypothetical protein 12, 80
Synpcc7942_1608 "mannose-6-phosphate isomerase, type 2 (EC 5.3.1.8) / mannose-1-phosphate guanylyltransferase (GDP) (EC 2.7.7.22) (IMGterm)" 80, 165
Synpcc7942_1654 hypothetical protein 43, 127
Synpcc7942_1736 Iron-regulated ABC transporter ATPase subunit SufC (IMGterm) 5, 43
Synpcc7942_1737 Iron-regulated ABC transporter permease protein SufD (IMGterm) 5, 43
Synpcc7942_1738 cysteine desulfurase (EC 2.8.1.7) (IMGterm) 5, 43
Synpcc7942_1739 "transcriptional regulator, MerR family (IMGterm)" 43, 124
Synpcc7942_1773 hypothetical protein 15, 80
Synpcc7942_1817 response regulator receiver domain protein (CheY-like) 80, 130
Synpcc7942_1846 hypothetical protein (EC:3.1.-) 43, 186
Synpcc7942_1847 dihydrodipicolinate synthase (EC 4.2.1.52) (IMGterm) 34, 43
Synpcc7942_1848 aspartate semialdehyde dehydrogenase (EC 1.2.1.11) (IMGterm) 43, 80
Synpcc7942_1956 acetyl-CoA carboxylase carboxyltransferase subunit alpha (IMGterm) 80, 138
Synpcc7942_1966 hypothetical protein 80, 145
Synpcc7942_2042 hypothetical protein 4, 80
Synpcc7942_2109 ATPase 80, 140
Synpcc7942_2148 ATPase 61, 80
Synpcc7942_2149 ABC-2 type transport system permease protein 61, 80
Synpcc7942_2174 "putative transcriptional regulator, Crp/Fnr family" 80, 86
Synpcc7942_2299 rpsO SSU ribosomal protein S15P (IMGterm) 43, 110
Synpcc7942_2302 hypothetical protein 43, 90
Synpcc7942_2345 conserved hypothetical protein YCF65 43, 112
Synpcc7942_2456 hypothetical protein 80, 118
Synpcc7942_2487 hypothetical protein 43, 84
Synpcc7942_2496 "amino acid/amide ABC transporter substrate-binding protein, HAAT family (TC 3.A.1.4.-) (IMGterm)" 14, 80
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_1521
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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