Organism : Methanococcus maripaludis S2 | Module List :
MMP0304

N-glycosylase/DNA lyase

CircVis
Functional Annotations (3)
Function System
Uncharacterized protein conserved in archaea cog/ cog
DNA-(apurinic or apyrimidinic site) lyase activity go/ molecular_function
DNA repair go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0304
(Mouseover regulator name to see its description)

MMP0304 is regulated by 12 influences and regulates 0 modules.
Regulators for MMP0304 (12)
Regulator Module Operator
H2 43 ef
MMP0052
MMP0097
43 combiner
MMP0097
MMP1100
43 combiner
MMP0168
MMP1100
43 combiner
MMP0097
MMP1015
22 combiner
H2 33 ef
MMP0499 33 tf
MMP0499
MMP1065
33 combiner
MMP0907
MMP1646
33 combiner
MMP1015 33 tf
MMP0097
MMP0527
152 combiner
MMP0460 152 tf

Warning: MMP0304 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 8 motifs predicted.

Motif Table (8)
Motif Id e-value Consensus Motif Logo
705 2.10e+01 AAc.CtTGTtaTgactGAAa
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706 6.20e+02 aTaagGttTtt.AAataAtAA
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727 3.20e-01 TgTaaAtttgGgGGtGagA
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728 2.60e+02 CggAATCTAGC
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747 0.00e+00 Ttg.agGgGGg
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748 2.80e+01 ACCCCtTctCAtatActCccG
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953 1.80e+00 tgctGGaGgaa
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954 5.30e+02 gAaccacacTccAAA
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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 MMP0304

MMP0304 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Uncharacterized protein conserved in archaea cog/ cog
DNA-(apurinic or apyrimidinic site) lyase activity go/ molecular_function
DNA repair go/ biological_process
Module neighborhood information for MMP0304

MMP0304 has total of 90 gene neighbors in modules 22, 33, 43, 152
Gene neighbors (90)
Gene Common Name Description Module membership
Antisense_10 None 2, 43, 150
Antisense_2 None 1, 22
Antisense_5 None 1, 22
MMP0008 DP1 DNA polymerase II small subunit 22, 75, 142
MMP0071 DNA primase small subunit 72, 152
MMP0085 hypothetical protein MMP0085 22, 106
MMP0102 pcm protein-L-isoaspartate O-methyltransferase 2, 43, 150
MMP0147 nitrogenase reductase-like protein 17, 22
MMP0172 hypothetical protein MMP0172 9, 43
MMP0177 hypothetical protein MMP0177 83, 117, 152
MMP0231 cysteine-rich small domain 145, 152
MMP0269 hypothetical protein MMP0269 76, 152
MMP0281 ATPase 22, 64
MMP0294 Pyrrolo-quinoline quinone 43, 125
MMP0304 N-glycosylase/DNA lyase 22, 33, 43, 152
MMP0305 2-oxoacid ferredoxin oxidoreductase subunit beta 2, 33, 43
MMP0306 oxidoreductase family protein member subunit alpha 2, 33, 43
MMP0307 hypothetical protein MMP0307 33, 49, 153
MMP0311 hypothetical protein MMP0311 33, 73
MMP0327 deoA thymidine phosphorylase 94, 152
MMP0453 neutral zinc metallopeptidase 22, 75
MMP0499 hypothetical protein MMP0499 22, 28, 144, 146, 153
MMP0547 RecJ-like protein 22, 166
MMP0570 hypothetical protein MMP0570 22, 65
MMP0585 UspA domain-containing protein 83, 151, 152
MMP0587 napA sodium/hydrogen exchanger 22, 69
MMP0599 cbiJ precorrin-6x reductase CbiJ/CobK 33, 152
MMP0600 hypothetical protein MMP0600 2, 33
MMP0614 iron-sulfur flavoprotein 43, 125, 151
MMP0634 hypothetical protein MMP0634 43, 108
MMP0660 apt adenine phosphoribosyltransferase 83, 94, 152
MMP0676 intermediate filament protein 145, 152
MMP0691 hypothetical protein MMP0691 33, 73
MMP0693 aminoacyl-tRNA synthetase, class II 33, 54
MMP0710 HAD superfamily ATPase 43, 159
MMP0711 corA magnesium/cobalt transporter CorA 43, 108
MMP0717 hypothetical protein MMP0717 22, 144
MMP0718 hypothetical protein MMP0718 35, 43
MMP0719 transcriptional regluator 35, 43
MMP0760 hypothetical protein MMP0760 22, 67, 92
MMP0761 hypothetical protein MMP0761 22, 64
MMP0762 hypothetical protein MMP0762 19, 43
MMP0763 hypothetical protein MMP0763 43, 123
MMP0783 hypothetical protein MMP0783 43, 160
MMP0784 hypothetical protein MMP0784 43, 163
MMP0792 membrane protein 9, 22
MMP0793 hypothetical protein MMP0793 9, 22
MMP0795 hypothetical protein MMP0795 22, 126
MMP0843 hypothetical protein MMP0843 22, 28
MMP0871 hypothetical protein MMP0871 22, 153, 166
MMP0903 hypothetical protein MMP0903 33, 54, 55
MMP0964 hypothetical protein MMP0964 43, 108
MMP0991 hypothetical protein MMP0991 22, 65
MMP0996 hypothetical protein MMP0996 43, 90, 125
MMP0997 blue (type1) copper domain-containing protein 23, 43, 90, 125
MMP1009 pyrC dihydroorotase 22, 142
MMP1029 hypothetical protein MMP1029 65, 152
MMP1059 hypothetical protein MMP1059 2, 22, 33
MMP1060 cysS cysteinyl-tRNA synthetase 33, 102
MMP1065 BadM/Rrf2 family transcriptional regulator 55, 152
MMP1228 hypothetical protein MMP1228 4, 22, 142
MMP1233 formate dehydrogenase family accessory protein FdhD 145, 152
MMP1234 UBA/THIF-type NAD/FAD binding protein 33, 54, 55, 106
MMP1236 hypothetical protein MMP1236 22, 55, 117, 142, 152
MMP1257 NERD domain-containing protein 19, 43
MMP1291 glycoside hydrolase family protein 43, 166
MMP1292 glycoside hydrolase 15-like protein 43, 166
MMP1293 group 1 glycosyl transferase 43, 159
MMP1294 glgA starch synthase 43, 150, 166
MMP1295 glucose-6-phosphate isomerase 43, 75
MMP1372 manB phosphomannomutase 49, 94, 152
MMP1387 hypothetical protein MMP1387 33, 73, 150
MMP1398 dapE diaminopimelate aminotransferase 22, 142
MMP1447 Cro repressor family protein 22, 117
MMP1452 ehaE hypothetical protein MMP1452 22, 117
MMP1453 ehaF hypothetical protein MMP1453 22, 117
MMP1477 cbiA cobyrinic acid a,c-diamide synthase 46, 152
MMP1487 gapN aldehyde dehydrogenase 55, 152
MMP1549 AP endonuclease 1, 94, 152
MMP1580 dihydropteroate synthase 22, 145, 152
MMP1597 phosphatidylglycerophosphatase A 22, 142, 144
MMP1604 hypothetical protein MMP1604 43, 166
MMP1619 molybdenum cofactor biosynthesis protein MoeA 117, 152
MMP1636 major facilitator transporter 22, 65, 153
MMP1683 hypothetical protein MMP1683 33, 73
MMP1686 cbf5 H/ACA RNA-protein complex component Cbf5p 22, 67
MMP1703 hypothetical protein MMP1703 43, 108
Unanno_13 None 33, 73
Unanno_39 None 23, 33
Unanno_57 None 43, 124
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 MMP0304
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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