{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Building a gene network from the IDR and STRINGdb\n", "This notebook exemplifies how to build Figure 1 of the paper\n", "using the IDR API." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Dependencies\n", " * [Matplotlib](http://matplotlib.org/)\n", " * [NumPy](http://www.numpy.org/)\n", " * [Pandas](http://pandas.pydata.org/)\n", " * [NetworkX](https://networkx.github.io/)\n", " * [Py2Cytoscape](https://pypi.python.org/pypi/py2cytoscape)\n", " * [Requests](http://docs.python-requests.org/)\n", " \n", "The cell below will install dependencies if you choose to run the notebook in [Google Colab](https://colab.research.google.com/notebooks/intro.ipynb#recent=true)." ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Requirement already satisfied: idr-py in /srv/conda/envs/notebook/lib/python3.7/site-packages 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"data": { "text/html": [ "\n", "
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If loading BokehJS from CDN, this \\n\"+\n", " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", " \"
\\n\"+\n", " \"\\n\"+\n",
" \"from bokeh.resources import INLINE\\n\"+\n",
" \"output_notebook(resources=INLINE)\\n\"+\n",
" \"
\\n\"+\n",
" \"\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"
\\n\"+\n \"\n", " | 0 | \n", "1 | \n", "2 | \n", "3 | \n", "4 | \n", "5 | \n", "6 | \n", "7 | \n", "8 | \n", "9 | \n", "10 | \n", "11 | \n", "12 | \n", "13 | \n", "14 | \n", "
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0 | \n", "string:9606.ENSP00000340896 | \n", "string:9606.ENSP00000267197 | \n", "ASH2L | \n", "SETD1B | \n", "- | \n", "- | \n", "- | \n", "- | \n", "- | \n", "taxid:9606 | \n", "taxid:9606 | \n", "- | \n", "- | \n", "- | \n", "score:0.999|ascore:0.088|escore:0.962|dscore:0... | \n", "
1 | \n", "string:9606.ENSP00000340896 | \n", "string:9606.ENSP00000264515 | \n", "ASH2L | \n", "RBBP5 | \n", "- | \n", "- | \n", "- | \n", "- | \n", "- | \n", "taxid:9606 | \n", "taxid:9606 | \n", "- | \n", "- | \n", "- | \n", "score:0.999|ascore:0.201|escore:0.975|dscore:0... | \n", "
2 | \n", "string:9606.ENSP00000369810 | \n", "string:9606.ENSP00000220509 | \n", "VPS16 | \n", "VPS18 | \n", "- | \n", "- | \n", "- | \n", "- | \n", "- | \n", "taxid:9606 | \n", "taxid:9606 | \n", "- | \n", "- | \n", "- | \n", "score:0.999|ascore:0.18|escore:0.943|dscore:0.... | \n", "
3 | \n", "string:9606.ENSP00000267197 | \n", "string:9606.ENSP00000264515 | \n", "SETD1B | \n", "RBBP5 | \n", "- | \n", "- | \n", "- | \n", "- | \n", "- | \n", "taxid:9606 | \n", "taxid:9606 | \n", "- | \n", "- | \n", "- | \n", "score:0.999|ascore:0.067|escore:0.962|dscore:0... | \n", "
4 | \n", "string:9606.ENSP00000325863 | \n", "string:9606.ENSP00000265335 | \n", "MRE11A | \n", "RAD50 | \n", "- | \n", "- | \n", "- | \n", "- | \n", "- | \n", "taxid:9606 | \n", "taxid:9606 | \n", "- | \n", "- | \n", "- | \n", "score:0.999|nscore:0.309|ascore:0.46|escore:0.... | \n", "
5 | \n", "string:9606.ENSP00000390475 | \n", "string:9606.ENSP00000264515 | \n", "CXXC1 | \n", "RBBP5 | \n", "- | \n", "- | \n", "- | \n", "- | \n", "- | \n", "taxid:9606 | \n", "taxid:9606 | \n", "- | \n", "- | \n", "- | \n", "score:0.998|ascore:0.054|escore:0.931|dscore:0... | \n", "
6 | \n", "string:9606.ENSP00000390475 | \n", "string:9606.ENSP00000340896 | \n", "CXXC1 | \n", "ASH2L | \n", "- | \n", "- | \n", "- | \n", "- | \n", "- | \n", "taxid:9606 | \n", "taxid:9606 | \n", "- | \n", "- | \n", "- | \n", "score:0.998|ascore:0.058|escore:0.953|dscore:0... | \n", "
7 | \n", "string:9606.ENSP00000390475 | \n", "string:9606.ENSP00000262519 | \n", "CXXC1 | \n", "SETD1A | \n", "- | \n", "- | \n", "- | \n", "- | \n", "- | \n", "taxid:9606 | \n", "taxid:9606 | \n", "- | \n", "- | \n", "- | \n", "score:0.998|ascore:0.181|escore:0.933|dscore:0... | \n", "
8 | \n", "string:9606.ENSP00000264515 | \n", "string:9606.ENSP00000262519 | \n", "RBBP5 | \n", "SETD1A | \n", "- | \n", "- | \n", "- | \n", "- | \n", "- | \n", "taxid:9606 | \n", "taxid:9606 | \n", "- | \n", "- | \n", "- | \n", "score:0.998|ascore:0.067|escore:0.916|dscore:0... | \n", "
9 | \n", "string:9606.ENSP00000362948 | \n", "string:9606.ENSP00000265350 | \n", "MED18 | \n", "MED20 | \n", "- | \n", "- | \n", "- | \n", "- | \n", "- | \n", "taxid:9606 | \n", "taxid:9606 | \n", "- | \n", "- | \n", "- | \n", "score:0.998|ascore:0.074|escore:0.833|dscore:0... | \n", "