Help
Below is a compilation of the help text from the web pages. Throughout the pages you can access the relevant help text by clicking on the buttons with the question mark.The EndoNet network
The figure bellow shows an abstract visualization of the EndoNet network.
- Hormone
- Messengers in the intercellular network. These may be classical hormones or other substances. They have to be secreted and need to have a target to transport a signal.
- Transport
- The Transport entity links a hormone to the receptor to which it binds. The linked Cell entity represents the transport medium like blood, not the target or source cell.
- Receptor
- The receptor is the first target of an hormone in a target cell. In the typical case the receptor is located in the cell membrane, but the receptor can also be located inside of the cell or even in the nucleus.
- Receptor-cell
- A receptor can be expressed in different cells, but may have tissue specific effects like the impact on the secretion of another hormone or a phenotype.
- Cell
- In EndoNet the source and target of the intercellular communication are cells, tissues and organs. For the annotation the most precise information is used, which may range from cellular level up to whole organs or larger anatomical structures. The anatomical structures used in EndoNet are linked to the Cytomer ontology. Using this ontology and the OBA service related anatomical structures are included in the search and on the detail pages.
- Influence
- The influence describes the influence of a hormone through binding to its receptor onto the next secretion step. The complete intracellular pathway is summarized by this entity or link.
- Secretion
- A hormone can be secreted from more than one cell type and each cell type can secrete several messengers. The secretion entity describes the secretion event of one hormone by one cell type.
- Phenotype / Phenotype trigger
- Besides of influencing the next secretion step a receptor activation can also change the state of the cell or organ. These changes can often be observed at a macroscopic level only. The phenotype can be tissue specific, being triggered by a specific receptor-cell combination, therefore the phenotype is linked via the entity Phenotype trigger to the receptor-cell combination. For EndoNet a phenotype is the endpoint of a signaling path.
- Ext. stimulus
- Like the phenotype is an endpoint of a pathway the external stimulus is a starting point. "External" in the scope of EndoNet is to be read as external of the endocrine system, not necessarily outside to the organism.
Search
The search pattern is searched in all names of the components. In the list
only the main name is displayed in the result lists.
For the anatomical structures also all available sub structures are listed.
If the query string is a valid EndoNet ID, you are redirected to the corresponding
detail page.
An EndoNet ID has the format ENX0000, where X stands for:
- H: Hormone
- R: Receptor
- C: Cell
The query string can also be appended to the end of the URL, e. g.
'http://endonent.bioinf.med.uni-goettingen.de/serach/growth factor'.
Adding items to the network
Through the toolbox, available on the navigation bar on the detail pages and near the links throughout the pages, EndoNet items can be added to and removed from an individual network. On the network processing page the added components can be reviewed and expanded to build a network.
Process network
Expanding components of the network
After adding EndoNet components to the user defined network, they should be expanded. This could be done on the page "Process the network" for single components in the table on the top or with all with the button "Expand" left to the table.
During a expansion not only the direct neighbors are added to the network, but all those nodes that are related to the node that is to be expanded.
Expanding a hormone node
When expanding a hormone its secretions and targets are added to the network. Upstream of the hormone the secretion event and the source cell are considered for the network. Other secretions of the source cell are not inserted as well as a possible influence of the secretion event. Downstream of the hormone the receptor, the receptor-cell combination and the target anatomical structure are added to the network. A possible influence to the secretion of the next hormone or the trigger of a phenotype is not considered.
Expanding a receptor node
Upstream of the receptor all binding hormones and the transports are added to the network This includes the transport medium if it is annotated. Downstream of the receptor the cell, that expresses the receptor is included as well as further downstream events that are triggered by the activation of the receptor. In more detail these are a potential influence on the secretion of the next hormone (without the hormone itself or the secreting cell) and the triggered potential phenotype. Other receptors of the target cells of the added receptor are ignored.
Expanding an anatomical structure (cell / tissue / organ) node
The expansion of a cell node adds the directly neighbors secretion and the receptor-cell combination containing the expanded cell. The secreted hormone is not considered. Also the receptors of the cells are only represented by the receptor cell combination. If the anatomical structure is included in a transport as transport medium the transported hormone and the target receptor are inserted into the network.
Expanding a receptor-cell combination node
For the expansion of the cell-receptor combination its direct neighbors are inserted into the network
Expanding a secretion or external stimulus
The expansion of a secretion or an external stiumli affects the same type of components. Downstream of secretion the hormone is inserted, upstream the influence of the corresponding receptor cell combination.
Expanding an influence node
The expansion of a influence includes the secretion of the downstream hormone and the upstream cell-receptor combination. Also the cell of the cell-receptor combination is added to the network. This cell will be also the source cell of the influenced hormone. However, the source cell of the hormone is not inserted by an expansion of the influence.
Expanding an phenotype / phenotype trigger node
For the expansion of a phenotype or a phenotype trigger the cell-receptor combination upstream of the phenotype is added to the network.
Expanding a transport node
The expansion of a transport node only affects the direct neighbors. These are hormone, receptor and cell (as transport medium)
Processing the network
Signal flow converter
Some nodes in EndoNet's network represent valuable information to the user, but are not required for a graph representing the signal flow. For instance, the influence node connects a receptor in a cell with a secretion and is documented by appropriate references. By definition the in- and outdegree of the influence node is one, so the node can be removed from the signal flow graph and the cell-receptor-combination is linked directly to the secretion. The signal flow converter does the following operations:
- It removes the influence node and connects the cell-receptor-combination to the secretion node. The effect of the influence node (positive or negative) is copied to the new edge.
- The receptor node is removed from the graph. Each incident hormone is linked to each cell-receptor-combination.
- The phenotype trigger node is removed and the triggering receptor-cell-combination is linked to each phenotype downstream of this combination.
