What do the different arrowheads mean in the figure below? Are there arrows upstream or downstream signalling?
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3$\begingroup$ Hi and welcome to Bio.SE! This is pretty standard notation. The arrowhead is a promotion, and flathead is an inhibition. $\endgroup$– JamesOct 18, 2019 at 17:39
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1$\begingroup$ Hi James! Thanks for the answer! Do you happen to know any resources in general for these notion? and other types of pathway like dotted lines and etc? $\endgroup$– TomOct 18, 2019 at 17:46
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$\begingroup$ i dont know the usage of dotted lines @Tom $\endgroup$– Always ConfusedOct 18, 2019 at 17:49
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$\begingroup$ There is an interesting proposal paper by Hiroaki Kitano. However all books should provide a table of all molecular biology notations and conventions but unfortunately these are not yet available. $\endgroup$– Always ConfusedOct 18, 2019 at 17:51
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4 Answers
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Arrowhead interpretation
As I said in my comment and to add to @AlwaysConfused's answer, the arrowhead is a promotion, and flathead is an inhibition.
Typically, any other notation such as dotted lines would be explained in the figure legend of the illustration.
The below definitions are generally accepted and widely used. But don't take these definitions for granted; there are no strict usage policies for these diagrams. Different groups may use different nomenclature and symbols.
These definitions were taken from a legend in cellsignal.com.
Upstream and downstream
The arrowheads are not necessarily linked to up and downstream signalling. Generally, the direction of the arrow indicates upstream/downstream. However, at a glance, this has even less standardisation than the arrowheads. Sometimes, like in the example in the question, upstream is generally at the top, and downstream is at the bottom. Other times it is from left to right, or right to left. There are many examples of cyclical events which the only way to tell is by following each arrow "path" for a particular signal.
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1$\begingroup$ Thank you this answer will help me greatly. $\endgroup$ Oct 25, 2019 at 4:15
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The blunt head arrow means inhibition i.e. suppression. i. e.
A -----------| B
means A suppressing B. the factor at the arrowhead is being supressed. The factor at arrowtail is an suppresor for the other factor.
The pointed head arrow means activation or increasing activity.
A -------------> B
means A is increasing activity of B. Factor at arrowhead is being activated. Factor at arrowtail is an activator for the other factor
answered Oct 18, 2019 at 17:37
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The "normal" (green here) arrowheads stand for a positive effect of the upstream factor or protein on the process or protein it points to. For instance, it means amino acids activate TORC1. Instead, arrows that end with a line (red here) stand for inhibition. For instance, rapamycin inhibits TORC1.
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Oxygen, amino acids , energy level and growth factors are activating TORC1 gene (growth factors also cause TORC2 activation).
Then further TORC1 gene promotes translation, cell cycle and metabolism, but inhibits autophagy. Whereas TORC2 promotes cellular metabolism and cytoskeleton. Rapamycin and Stress inhibits TORC1.
Green arrow is used to show stimulatory effect and Red flathead is used for showing inhibiting effect.
These arrows have nothing to do with upstream and downstream signalling.
Read further about this https://www.khanacademy.org/science/biology/cell-signaling/mechanisms-of-cell-signaling/a/intracellular-signal-transduction
