Network updates

Upgraded to hetio-ind commit to dhimmel/integrate@f72d32c. Gene-disease associations were renamed to variations. Functions are now called associations. Abbreviated Illumina for facet title. Entrez gene download in `network-degrees.ipynb` no longer needed.
dhimmel · Sep 1, 2015 · 0659caa · 0659caa
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diff --git a/README.md b/README.md
@@ -47,5 +47,5 @@ This analysis can be reproduced by running the Jupyter notebooks in the followin
 1. [`network-degrees.ipynb`](network-degrees.ipynb) to extract gene degrees from [hetio-ind](https://github.com/dhimmel/integrate), a hetnet that includes many gene metaedges.
 2. [`SNP-to-Gene.ipynb`](SNP-to-Gene.ipynb) to download data and perform processing for SNP chips.
 3. [`exac.ipynb`](exac.ipynb) to process the [ExAC](http://exac.broadinstitute.org/) sequencing variants.
-4. [`combine-SNPs-with-degrees.ipynb`](combine-SNPs-with-degrees.ipynb) to combine SNPs per Gene measurements from all platforms and hetnet degrees.
+4. [`combine-SNPs-and-degrees.ipynb`](combine-SNPs-and-degrees.ipynb) to combine SNPs per Gene measurements from all platforms and hetnet degrees.
 5. [`visualization.ipynb`](visualization.ipynb) to create visualizations. This is an [R notebook](https://github.com/IRkernel/IRkernel).
diff --git a/combine-SNPs-with-degrees.ipynb → combine-SNPs-and-degrees.ipynb b/combine-SNPs-with-degrees.ipynb → combine-SNPs-and-degrees.ipynb
diff --git a/data/combined.tsv.gz b/data/combined.tsv.gz
diff --git a/data/gene-degrees.tsv.gz b/data/gene-degrees.tsv.gz
diff --git a/download/network-summary.tsv b/download/network-summary.tsv
@@ -1,27 +1,27 @@
 metaedge	abbreviation	inverted	edges	source_nodes	target_nodes	unbiased
-gene - binding - compound	GbC	1	2502	572	554	0
+gene - participation - pathway	GpPW	0	79101	9511	1615	0
+gene - downregulation - compound	GdC	1	20312	923	748	20312
+gene - variation - disease	GvD	1	1284	926	91	1284
+gene - expression - anatomy	GeA	0	987862	18041	194	914193
+gene - downregulation - disease	GdD	1	674	664	3	674
+gene - participation - biological process	GpBP	0	534004	14533	11014	0
+gene < knockdown downregulation < gene	G<kdG	1	140942	957	4207	140942
 gene - upregulation - compound	GuC	1	17261	953	729	17261
 gene < knockdown upregulation < gene	G<kuG	1	78752	970	4068	78752
-gene - participation - biological process	GpBP	0	534004	14533	11014	0
-gene - upregulation - anatomy	GuA	0	97848	15929	36	97848
-gene - interaction - gene	GiG	0	297253	15211	15211	31575
+gene - participation - molecular function	GpMF	0	93857	12890	2826	0
 gene > overexpression downregulation > gene	God>G	0	14911	1660	830	14911
+gene > knockdown downregulation > gene	Gkd>G	0	140942	4207	957	140942
+gene > overexpression upregulation > gene	Gup>G	0	15292	1862	909	15292
 gene - participation - cellular component	GpCC	0	65377	10269	1332	0
-gene > knockdown upregulation > gene	Gku>G	0	78752	4068	970	78752
+gene - evolution - gene	GeG	0	123382	12453	12453	123382
 gene - target - compound	GtC	1	4603	1133	1182	0
-gene < knockdown downregulation < gene	G<kdG	1	140942	957	4207	140942
-gene > overexpression upregulation > gene	Gup>G	0	15292	1862	909	15292
-gene - function - disease	GfD	1	10193	3701	103	0
 gene < overexpression downregulation < gene	G<odG	1	14911	830	1660	14911
-gene - participation - molecular function	GpMF	0	93857	12890	2826	0
-gene > knockdown downregulation > gene	Gkd>G	0	140942	4207	957	140942
+gene - upregulation - anatomy	GuA	0	97848	15929	36	97848
 gene - regulation - perturbation	GrPB	0	366502	18245	3395	0
-gene < overexpression upregulation < gene	G<upG	1	15292	909	1862	15292
 gene - upregulation - disease	GuD	1	910	870	3	910
+gene < overexpression upregulation < gene	G<upG	1	15292	909	1862	15292
+gene - binding - compound	GbC	1	2502	572	554	0
+gene - association - disease	GaD	1	11824	5067	134	0
+gene > knockdown upregulation > gene	Gku>G	0	78752	4068	970	78752
+gene - interaction - gene	GiG	0	297253	15211	15211	31575
 gene - downregulation - anatomy	GdA	0	102240	15097	36	102240
-gene - expression - anatomy	GeA	0	987862	18041	194	914193
-gene - participation - pathway	GpPW	0	79101	9511	1615	0
-gene - evolution - gene	GeG	0	123382	12453	12453	123382
-gene - downregulation - disease	GdD	1	674	664	3	674
-gene - downregulation - compound	GdC	1	20312	923	748	20312
-gene - association - disease	GaD	1	1284	926	91	1284
diff --git a/figure/adj-degree-v-snps.pdf b/figure/adj-degree-v-snps.pdf
diff --git a/figure/adj-degree-v-snps.png b/figure/adj-degree-v-snps.png
diff --git a/figure/adj-degree-v-snps.svg b/figure/adj-degree-v-snps.svg
diff --git a/figure/degree-v-snps-all.pdf b/figure/degree-v-snps-all.pdf
diff --git a/figure/degree-v-snps-all.png b/figure/degree-v-snps-all.png
diff --git a/figure/degree-v-snps-all.svg b/figure/degree-v-snps-all.svg
diff --git a/figure/degree-v-snps.pdf b/figure/degree-v-snps.pdf
diff --git a/figure/degree-v-snps.png b/figure/degree-v-snps.png
diff --git a/figure/degree-v-snps.svg b/figure/degree-v-snps.svg