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The Filter by Flags functionality for Affymetrix data could be used when you are working with. CHP files. The CHP files contain the flag information. There are two factors based on which the filtering is done here. The percentile cutoff and the filter criteria of in how many samples must a probe set have intensity value within the specified range. Together, these two factors will determine what kind of probe sets is eliminated.

We try to set this percentile cutoff to only eliminate genes that are not expressed. What we are saying is that if an intensity value of a probe set is below the 20th percentile in that sample, the gene is probably not expressed in that sample.

It is known that any given tissue, not all genes in the human genome is expressed. If probe sets were filtered such that they must have values within the range above 20th percentile in all samples or in both conditions , then there is a possibility of interesting genes being excluded.

Thus, potentially interesting biological changes between experimental conditions could be missed. To decrease the chances of missing these changes, the stringency of the filter is set such that even if the gene is only expressed in one sample in the experiment, the probe set will pass the filter.

But, this criterion could be changed by the user according to their interest. Flags are attributes that denote the quality of the entities. Using these attribute values in GeneSpring we filter the genes. These values are generated based on the feature quality on the chip, like signal saturation and signal uniformity. The genes which are given low significant attribute in the data file would be marked as 'Absent' and high significant values would be marked as 'Present'. These flags are generally specific to the technology or the array type used.

Thus the experiment technology type, i. This information can be viewed by selecting the Filter on Data files option under Quality Control. This error indicates that some of the required library files are not present. Accept the License Agreement by clicking Yes. The missing libraries are installed. You need to restart GeneSpring for the changes to take effect.

Yes, genes in an experiment can be mapped to chromosomal location in Genome Browser of GeneSpring. The mapping is based on chromosome number, start and end locations.

To run Genome Browser, please download the build for the organism of your experiment. Select the Organism and build of your interest and download them and then try to run Genome Browser. GeneSpring provides you with the option to create your organism and build in the tool. Chromosome name and length without any header should be present in a file for creating a build. For example chr1 chr2 You may contact GeneSpring support to obtain a file based update.

It will list all the annotations present in the update file, select the interested ones and click update. Yes, you can select a specific region in a chromosome in either of the following ways: a.

Enter the region of interest in the chromosomal coordinates b. Browse through the chromosome : Below are the options to browse through the chromosome in Genome Browser:. The selected entity will be highlighted in the spreadsheet as well as the tracks.

Data from different experiments can be plotted on Genome Browser. To view the data, drag and drop the entity lists of interest on Genome Browser, it will be added as a track and can be viewed along with the other existing tracks. Yes, it is possible to view list associated values p-value, Fold change, etc on Genome Browser. Select the required data and it will be added in the same track as one more feature.

Click ok. List associated values are also shown in the spreadsheet. The mapping of probes in Genome Browser is done using chromosome number and location.

The chromosome number is expected to be in alphanumeric chr1 or only numeric characters. If the format is alphanumeric then all the alphabets should be lowercase. The error could occur if the chromosome number has uppercase in them.

The Genome Browser is launched on the organism of your experiment. Check the organism of your experiment to ensure that it is the same as the organism of the build. You have the option to change the organism in the Technology Inspector window.

Yes, the builds will continue to work. Following this, select the track of interest and arrange it in the order of preference using up or down arrow.

Merge icon is used to bring different tracks together. This option is highlighted when two data tracks are selected and both tracks have only one feature enabled.

Data distribution over all chromosomes can be obtained by editing track properties from Right-click operations. This will show the data for the selected chromosome in Genome browser area. Similar is the case if you wish to view data for a particular feature for the whole genome. Right-click on the track of interest and select Edit track properties.

Go to Genome View and select the required feature and click ok. It will enable this feature in Genome View. Yes, annotation information present in a file can be imported in GeneSpring. You may use any of the following methods:. To export a list of probes to eArray, right-click on the chosen entity list in the Experiment Navigator and select Export to eArray. Yes, you need to have an account and associated log in information for the eArray portal in order to submit a probe list.

Yes, it is possible to export either all or a selection of entities displayed in a pathway to eArray. To export the list, right-click the Pathway Viewer and select Export to eArray.

In the Export to eArray dialog, choose whether you want to export all entities or only the selected entities and the experiment type Expression or RNA Enrichment.

When exporting pathway entities to eArray, only 'GenBank Accession' data can be exported. The Export to eArray functionality in GeneSpring allows you to export a maximum of 10, genomic coordinates or GenBank Accession numbers.

The metadata framework allows you to visualize sample parameters like administrative data, sample parameters, or others alongside your clustered experiment data in the form of sample parameter plots.

GeneSpring 13 allows you to plot parameter values in a clustering view. To be able to see stage information, please enter the staging information as a new parameter through the Experiment Grouping functionality available from the Workflow Browser.

Select the type of plot you want to use to display the staging parameter, for example Heatmap. Yes, the plots can be exported. They are exported as part of the cluster tree export. The next step will allow you to select individually which sample parameter plots that you would like to export. Yes, you can run correlation analysis on the entities of your interest in GeneSpring Correlation analysis in quality control on samples operates on all entities and all samples and is calculated using Pearson correlation.

However, correlation under analysis allows you to perform sample level correlation on the entity list of your interest. You could also limit the correlation calculation on a specific set of samples as defined in an interpretation. In addition to Pearson similarity, GeneSpring also provides you with the Spearman method of correlation co-efficient calculation.

Yes, you can perform correlation analysis on a combination of up to two omics types. Create an MOA experiment with the two corresponding experiments. Please note: the two experiments have to be in the same project to be able to create an MOA experiment.

The icon can be found on the extreme left of the correlation heatmap view toolbar. This is the first icon from the right in the correlation heatmap view toolbar. You can choose to export either all the correlation values, values for a filtered list or only highlighted entities. All Target Prediction databases have to be downloaded prior to analysis. If you are unable to obtain the updates from the Agilent server, for example due to internet connectivity issues, you can contact GeneSpring support to obtain file based updates.

The filters have to be changed in the Options window before starting the analysis to be applied. GeneSpring applies these filter settings to all subsequent analyses until you change them again in the Options window. Yes, it is required to download the new version of the TargetScan database in GeneSpring The old version of the database will not work in GeneSpring Similarly, you have to download any of the other Target Prediction databases available from GeneSpring The hypergeometric method is used for calculating p-values for target genes.

This is a new feature introduced in GeneSpring Yes, you can identify target genes that are present in the databases of your interest using the Find Targeted Genes option from the Results Interpretations section of the Workflow Browser by following these steps:.

In order to perform pathway analysis on any of your entity lists or selected entities in GeneSpring If you downloaded any Interaction Databases in a previous version of GeneSpring, we recommend that you update them.

All the Interaction Databases have been updated to include more entities and relations along with updated annotations for existing entities and relations. Obsolete entities and relations were removed. From GeneSpring Once such an update becomes available you will be notified the next time you start GeneSpring. Existing pathways will not be affected during the update.

Once the Interaction Databases are updated, the Update Pathways dialog will allow you to update your existing pathways by removing obsolete entities or relations and updating entities in case the name was changed. If you are planning to use non-GPML pathways, you should have enough disk space for downloading the Interaction Databases. The amount of disk space required will be approximately three times mentioned in the update window.

The BridgeDb algorithm allows GeneSpring to map entities if only differing annotations e. To import pathways from BioCyc www. You have to save this file to your computer and point to it in the Please Select A. The remaining steps are the same as described above. This dialog allows you to choose which of the pathways that you previously imported into GeneSpring non-GPML format only you would like to update or delete based on the new information recorded in the updated Interaction Database.

For each pathway the Update Pathways dialog displays updated entities and obsolete entities. Yes, deleting a pathway in the Update Pathway dialog will delete the pathway from any experiment it is saved in, as it is permanently deleted from the GeneSpring database. When importing pathways in the GPML format, GeneSpring identifies duplicate pathways based on pathway name, organism and pathway provider.

If duplicate pathways are found, the Resolve Duplicates dialog gives you the choice to. However, to import and work with any other file format, the common as well as the organism specific Interaction Databases are required. Single Experiment Analysis provides an option to select the pathway source in Step 1 of the wizard-driven workflow. To be able to work with KEGG pathways: a. A pathway node in KEGG pathway is grayed out if that entity is absent in the organism of your experiment. Some nodes in KEGG pathways may represent multiple entities.

For example, different isoforms of the protein, subunits of proteins, members of the same gene family, etc. All entities under the node get selected when you select the node on the pathways. Mouse over the node of interest to view all the entities under the node in the tooltip. You can also select the node to filter the heatmap below to limit it to only the entities represented by the node. Specific entities under the node can then be selected from the heatmap.

The annotation information on pathway nodes can be found in the Entity Properties dialog. Double-click on the node to open the corresponding dialog.

The annotation types in bold are the annotations that are supported for mapping pathway entities of the respective experiment type in GeneSpring. SEA identifies matching pathways for the entities of one experiment, compared to two experiments in an MOA.

But unlike in the previous FSP workflow, you can now choose a differing organism for pathway analysis from the organism associated with your chosen experiment and specify an experiment interpretation as well as preferred annotations. In addition, the new curated pathways options WikiPathways and pathways in. Please refer to Q1. What is Single Experiment Analysis? If column marks were inappropriately assigned at that time then you may encounter this issue. Please refer to section 3.

Yes, you can change the p-value cut-off after saving the results of the analysis in the form of a pathway list at the end of the Single Experiment workflow. Filters are available for both p-value and number of matching entities in a filter panel, which is located under pathway list panel in the left bottom corner of the Pathway View of an open pathway list. Yes, in Step 1 of 4 of the Single Experiment Analysis workflow, you can select what kinds of pathways available for the chosen organism are queried during Pathway Analysis depending on whether you would like to include only Curated pathways , or Literature Derived Networks , or both.

In GeneSpring This includes a set of 21 pathways that are packaged with your GeneSpring installation. One of the features of Pathway Analysis in GeneSpring is that experiment data associated with matching entities between the pathway and the chosen entity list is displayed in the form of Heatstrips next to the entities in the pathway viewer. By selecting an interpretation, Heatstrips will display the data according to the experimental conditions specified in the selected interpretation.

Yes, you can custom save selected pathways in Step 3 of 4 of the Multi-Omic Analysis workflow. The selected pathways are saved as a pathway list in a new MOA experiment, which is saved in the same project as the two input experiments. A Pathway List resulting from an MOA workflow contains all the pathways that were previously imported into GeneSpring of the selected pathway type and organism that were chosen in Step 1 of 4 of the MOA workflow. Use the Filter Panel options to identify significant pathways for the chosen entity lists.

Right-click the pathway list table at the top left of the Pathway View and select the desired option from the Export As submenu. Please note that exporting the table as an Image, or HTML only exports the visible pathway list panel area, while exporting it as a Text file exports the contents of the pathway list panel as a table.

You can create a Venn Diagram to illustrate common pathways. GeneSpring applies Homologene translation for genes for matching experiment entities with pathway entities when the selected pathway organism is different from the experiment organism. Grey cells indicate missing values. The Heatmap table in the Pathway View shows lists all the pathway entities of the same type as that of the input experiment. However, data values are only shown for matching entities with the input experiment.

Yes, you can view data from a different group of conditions by clicking the Choose another Interpretation icon and selecting another interpretation. Please note that this selection and the associated changes in the Pathway Viewer and the Heatmap table are not saved when the pathway list is closed. GeneSpring provides an option to view a Profile Plot of your genes of interest in a pathway.

To use this feature, select the genes of interest either from the pathway viewer or the Heatmap table and then click on the Launch Profile Plot icon from the Pathway View Toolbar. A continuous numerical or non-continuous categorical plot is displayed in a new window based on the interpretation selected during the pathway analysis workflow.

By default, the Heatstrips displayed in the Pathway Viewer and in the Heatmap table are normalized signal values. To view raw signal values instead, follow these steps:. The Heatstrips in the Pathway Viewer and the Heatmap table now display the raw signal values for matching entities between the pathway and the experiment.

Follow the steps below to create your organism and import relevant pathway files:. This workflow will result in a new pathway. The identified interactions will not be added to the existing pathway. To use this feature, follow these steps:. When adding a new entity to a pathway with the Add entity icon, either while creating a new pathway or during one of the NLP Networks workflows, the only required property is ' Synonym '.

GeneSpring uses this property to search the appropriate Interaction Databases for a match. If the entity already exists in one of the Interaction Databases, GeneSpring prevents you from adding the entity through this process. To add such an entity to the pathway, drag the symbol that represents the desired entity type in the Entity Legend into the Pathway Viewer and type the same term in the Search dialog that opens.

Select the appropriate entity from the search results and click OK. If GeneSpring does not find a match for the ' Synonym ' property that you provided you can continue creating this new entity by adding as many properties as possible. The ' Synonym ' property is not used for this purpose.

Yes, you can query such pathways. No, it is not possible to make any modifications to an entity after it was added to the Interaction Database.

To find out if an entity is already present in an Interaction Database, drag the symbol that represents the desired entity type in the Entity Legend into the Pathway Viewer and type the term by which this entity is most commonly referred to in the Search dialog that opens.

The search results will display all the matching entities GeneSpring found in the Interaction Databases. If the search result contains the entity you would like to add to the pathway, select the corresponding row and click OK. If the entity of interest is not present in the search result, leave the Search dialog and use the Add entity icon in the Pathway View Toolbar to create the entity with the information you have about this new entity.

The Color by Venn feature is used to differentiate entities in an open Profile Plot , Scatter Plot , or Cy3 vs Cy5 Plot based on the presence of these entities in the different regions of a Venn Diagram. The Profile Plot will not change if none of the entities that it contains are present in the selected Venn Diagram. To undo the effect of Color by Venn , relaunch the respective plot and its rendering will return to the original status.

For version Depending on the size of your data for example if you have previously downloaded interaction databases of multiple organisms , this process can take several hours. The information dialog guiding you through the update and migration process provides estimated size requirements and informs you if the available space in the GeneSpring installation directory is not sufficient.

The MySQL folder will remain untouched after migration. Therefore the total space requirement is approximately 2. If any other application on your computer is using the same port at the time you started GeneSpring, the PostgreSQL database will not have been able to startup. Save the file and launch GeneSpring again. Note: Not all applications use fixed ports, but might randomly choose a free port to run.

Therefore, this issue can occur again at a later time, even if you have changed the port once. If this is the case, just repeat the instructions here to change the port again.

You can manually change the permission settings using the chmod command. This will set the permissions for you to have read, write to, and execute permissions for the PostgreSQL folder. Frequently Asked Questions. Is it possible to check out module specific licenses? To use this feature, you need to have the following: Floating License Server for version GeneSpring Can I stop a user from using the Floating License Server?

What changes should users make to their clients in order to access the new Floating License Server? Enter username and password. Please refer to the manual for the same. Wait for confirmation that activation was successful. Once license activation is complete, start the server by clicking on Start service. If you face problems in activating the License Server, contact Support Manual activation for the Floating License Server In case you do not have web access from the License Server or if you face problems activating the License Server automatically, you will need to do the above step manually.

In response, the strand. Enter the IP address of the Floating Server machine to connect. WorkGroup License To activate the license contact us.