add coverage, lower stringency

mtinti · Jul 31, 2020 · d8b2685 · d8b2685
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commit d8b2685
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Showing 39 changed files with 487,407 additions and 13,239 deletions.
diff --git a/BACE1.html b/BACE1.html
diff --git a/Fig1.png b/Fig1.png
diff --git a/Fig1.svg b/Fig1.svg
diff --git a/Fig2.png b/Fig2.png
diff --git a/Fig2.svg b/Fig2.svg
diff --git a/MDS.png b/MDS.png
diff --git a/analysis_def.html b/analysis_def.html
diff --git a/analysis_def.ipynb b/analysis_def.ipynb
diff --git a/analysis_def_files/analysis_def_11_0.png b/analysis_def_files/analysis_def_11_0.png
diff --git a/analysis_def_files/analysis_def_14_0.png b/analysis_def_files/analysis_def_14_0.png
diff --git a/analysis_def_files/analysis_def_15_1.png b/analysis_def_files/analysis_def_15_1.png
diff --git a/analysis_def_files/analysis_def_17_0.png b/analysis_def_files/analysis_def_17_0.png
diff --git a/analysis_def_files/analysis_def_18_1.png b/analysis_def_files/analysis_def_18_1.png
diff --git a/analysis_def_files/analysis_def_37_4.png b/analysis_def_files/analysis_def_37_4.png
diff --git a/analysis_def_files/analysis_def_40_4.png b/analysis_def_files/analysis_def_40_4.png
diff --git a/analysis_def_files/analysis_def_42_4.png b/analysis_def_files/analysis_def_42_4.png
diff --git a/analysis_def_files/analysis_def_43_1.png b/analysis_def_files/analysis_def_43_1.png
diff --git a/analysis_def_files/analysis_def_44_4.png b/analysis_def_files/analysis_def_44_4.png
diff --git a/analysis_def_files/analysis_def_45_4.png b/analysis_def_files/analysis_def_45_4.png
diff --git a/analysis_def_files/analysis_def_48_1.png b/analysis_def_files/analysis_def_48_1.png
diff --git a/analysis_def_files/analysis_def_48_4.png b/analysis_def_files/analysis_def_48_4.png
diff --git a/analysis_def_files/analysis_def_49_4.png b/analysis_def_files/analysis_def_49_4.png
diff --git a/analysis_def_files/analysis_def_51_1.png b/analysis_def_files/analysis_def_51_1.png
diff --git a/analysis_def_files/analysis_def_52_1.png b/analysis_def_files/analysis_def_52_1.png
diff --git a/database/README.txt b/database/README.txt
@@ -0,0 +1,2 @@
+download link on 28/07/20
+https://www.uniprot.org/proteomes/UP000000589
diff --git a/database/bait.fa b/database/bait.fa
@@ -0,0 +1,15 @@
+>BACE1-BirA fusion protein DNA sequence
+MAQALPWLLLWMGAGVLPAHGTQHGIRLPLRSGLGGAPLGLRLPRETDEEPEEPGRRGSFV
+EMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYR
+DLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLA
+YAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSL
+YTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAA
+VKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQY
+LRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFR
+TAAVEGPFVTLDMEDCGYNIPQTDESTLMTIAYVMAAICALFMLPLCLMVCQWRCLRCLRQ
+QHDDFADDISLLKGGSGGSKDNTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTL
+RDWGVDVFTVPGKGYSLPEPIQLLNAKQILGQLDGGSVAVLPVIDSTNQYLLDRIGELKSG
+DACIAEYQQAGRGGRGRKWFSPFGANLYLSMFWRLEQGPAAAIGLSLVIGIVMAEVLRKLG
+ADKVRVKWPNDLYLQDRKLAGILVELTGKTGDAAQIVIGAGINMAMRRVEESVVNQGWITL
+QEAGINLDRNTLAAMLIRELRAALELFEQEGLAPYLSRWEKLDNFINRPVKLIIGDKEIFG
+ISRGIDKQGALLLEQDGIIKPWMGGEISLRSAEKA
diff --git a/database/uniprot-proteome UP000000589.fasta b/database/uniprot-proteome UP000000589.fasta
diff --git a/missing.png b/missing.png
diff --git a/only_bait.csv b/only_bait.csv
diff --git a/res_24.csv b/res_24.csv
diff --git a/res_48.csv b/res_48.csv
diff --git a/txt/indata_ProtRank.csv b/txt/indata_ProtRank.csv
diff --git a/txt/peptides.zip b/txt/peptides.zip
diff --git a/txt/prs-bait_vs_control_24.dat b/txt/prs-bait_vs_control_24.dat
diff --git a/txt/prs-bait_vs_control_48.dat b/txt/prs-bait_vs_control_48.dat
diff --git a/txt/prs-significant-bait_vs_control_24.dat b/txt/prs-significant-bait_vs_control_24.dat
@@ -1,61 +1,51 @@
-# list of 60 proteins with FDR <= 0.1 (FDR values computed using 100 bootstrap realizations of the data)
-BACE1-BirA
+# list of 50 proteins with FDR <= 0.1 (FDR values computed using 100 bootstrap realizations of the data)
 sp|Q80UU9|PGRC2_MOUSE
+BACE1-BirA
 sp|P49817|CAV1_MOUSE
 sp|Q9CQW9|IFM3_MOUSE
 sp|P63024|VAMP3_MOUSE
 sp|Q9CQW1|YKT6_MOUSE
-tr|A0A0R4J1G9|A0A0R4J1G9_MOUSE
 tr|A0A0J9YTY0|A0A0J9YTY0_MOUSE
-sp|O54724|CAVN1_MOUSE
+tr|A0A0R4J1G9|A0A0R4J1G9_MOUSE
 sp|O09044|SNP23_MOUSE
 tr|F7DBB3|F7DBB3_MOUSE
-tr|E9Q616|E9Q616_MOUSE
-sp|Q5Y5T1|ZDH20_MOUSE
+sp|O54724|CAVN1_MOUSE
 tr|D3YVM2|D3YVM2_MOUSE
+sp|Q5Y5T1|ZDH20_MOUSE
 sp|Q811D0|DLG1_MOUSE
+tr|A0A140LIU9|A0A140LIU9_MOUSE
 sp|Q80Z96|VANG1_MOUSE
 sp|Q6P9J9|ANO6_MOUSE
 sp|Q63918|CAVN2_MOUSE
-sp|O54962|BAF_MOUSE
-sp|P47738|ALDH2_MOUSE
+sp|Q3UL36|ARGL1_MOUSE
+tr|Q924U4|Q924U4_MOUSE
 sp|Q03145|EPHA2_MOUSE
 sp|P18572|BASI_MOUSE
+sp|Q62371|DDR2_MOUSE
+sp|P47738|ALDH2_MOUSE
+tr|E9Q9C3|E9Q9C3_MOUSE
+sp|O54962|BAF_MOUSE
 tr|A0A1B0GRR3|A0A1B0GRR3_MOUSE
+tr|A0A0A0MQM0|A0A0A0MQM0_MOUSE
 sp|Q3T9E4|TGTP2_MOUSE
+tr|E9Q616|E9Q616_MOUSE
+sp|Q8CIB5|FERM2_MOUSE
 sp|P43275|H11_MOUSE
-sp|Q62371|DDR2_MOUSE
-sp|P23242|CXA1_MOUSE
-sp|P50544|ACADV_MOUSE
 tr|Q9ESU7|Q9ESU7_MOUSE
-tr|E9Q9C3|E9Q9C3_MOUSE
-tr|A0A0A0MQM0|A0A0A0MQM0_MOUSE
-tr|Q3UXD9|Q3UXD9_MOUSE
 tr|A0A338P6B4|A0A338P6B4_MOUSE
-sp|Q8CIB5|FERM2_MOUSE
-sp|P45952|ACADM_MOUSE
-sp|Q08509|EPS8_MOUSE
+sp|P50544|ACADV_MOUSE
+sp|P23242|CXA1_MOUSE
+tr|E9Q3N1|E9Q3N1_MOUSE
+sp|Q8JZM0|TFB1M_MOUSE
 sp|Q8C0J6|SWAHC_MOUSE
-sp|Q8VCR7|ABHEB_MOUSE
-tr|F8WHG5|F8WHG5_MOUSE
 sp|Q922W5|P5CR1_MOUSE
 sp|P47962|RL5_MOUSE
+sp|P70453|PDE7A_MOUSE
+sp|P45952|ACADM_MOUSE
 tr|Q8VCV2|Q8VCV2_MOUSE
+tr|A0A498WFS2|A0A498WFS2_MOUSE
+tr|A2A6U3|A2A6U3_MOUSE
+tr|F8WHG5|F8WHG5_MOUSE
 sp|Q6ZQI3|MLEC_MOUSE
-sp|P10922|H10_MOUSE
-sp|Q99JR1|SFXN1_MOUSE
+tr|Q3UXD9|Q3UXD9_MOUSE
 sp|Q9CQU0|TXD12_MOUSE
-tr|E9Q3N1|E9Q3N1_MOUSE
-tr|V9GXA5|V9GXA5_MOUSE
-sp|Q04750|TOP1_MOUSE
-sp|Q8BKX1|BAIP2_MOUSE
-sp|Q3THW5|H2AV_MOUSE
-sp|Q9CZE3|RAB32_MOUSE
-tr|A2A6U3|A2A6U3_MOUSE
-sp|Q91YT8|CSCL1_MOUSE
-sp|P0CL69|ZN703_MOUSE
-sp|Q9EQ06|DHB11_MOUSE
-sp|Q9JHS4|CLPX_MOUSE
-sp|Q02013|AQP1_MOUSE
-sp|Q62093|SRSF2_MOUSE
-tr|A2ACM0|A2ACM0_MOUSE
diff --git a/txt/prs-significant-bait_vs_control_48.dat b/txt/prs-significant-bait_vs_control_48.dat
@@ -1,38 +1,33 @@
-# list of 37 proteins with FDR <= 0.1 (FDR values computed using 100 bootstrap realizations of the data)
+# list of 32 proteins with FDR <= 0.1 (FDR values computed using 100 bootstrap realizations of the data)
 sp|Q80UU9|PGRC2_MOUSE
-sp|P49817|CAV1_MOUSE
 sp|Q9CQW1|YKT6_MOUSE
 sp|P63024|VAMP3_MOUSE
-BACE1-BirA
-sp|O54724|CAVN1_MOUSE
+sp|P49817|CAV1_MOUSE
 sp|Q9CQW9|IFM3_MOUSE
 tr|A0A0J9YTY0|A0A0J9YTY0_MOUSE
+BACE1-BirA
+sp|O54724|CAVN1_MOUSE
 tr|A0A0R4J1G9|A0A0R4J1G9_MOUSE
 sp|P18572|BASI_MOUSE
 sp|Q811D0|DLG1_MOUSE
-sp|Q08509|EPS8_MOUSE
 sp|O09044|SNP23_MOUSE
-tr|E9Q616|E9Q616_MOUSE
 sp|Q5Y5T1|ZDH20_MOUSE
 tr|F7DBB3|F7DBB3_MOUSE
-sp|Q8BVY0|RL1D1_MOUSE
 tr|A2A6U3|A2A6U3_MOUSE
-tr|A0A494BAX5|A0A494BAX5_MOUSE
 sp|Q9WVA4|TAGL2_MOUSE
-sp|Q99JR1|SFXN1_MOUSE
 sp|Q8CIB5|FERM2_MOUSE
-sp|Q8C3W1|CA198_MOUSE
 sp|Q03145|EPHA2_MOUSE
 sp|Q80Z96|VANG1_MOUSE
 tr|A0A2U3TZ82|A0A2U3TZ82_MOUSE
+tr|E9Q9C3|E9Q9C3_MOUSE
 tr|Q9ESU7|Q9ESU7_MOUSE
-tr|Q3TQ29|Q3TQ29_MOUSE
-sp|Q61768|KINH_MOUSE
 sp|Q62371|DDR2_MOUSE
-sp|Q5F2E8|TAOK1_MOUSE
-tr|E9Q9C3|E9Q9C3_MOUSE
-sp|Q8VIG0|ZCH14_MOUSE
-sp|P08752|GNAI2_MOUSE
+sp|Q61768|KINH_MOUSE
+sp|Q8BVY0|RL1D1_MOUSE
+tr|E9Q616|E9Q616_MOUSE
 tr|E9QM38|E9QM38_MOUSE
-sp|Q8VDP4|CCAR2_MOUSE
-sp|P47962|RL5_MOUSE
+tr|A0A494BAX5|A0A494BAX5_MOUSE
+sp|Q99JR1|SFXN1_MOUSE
+sp|Q8R326|PSPC1_MOUSE
+sp|Q8C3W1|CA198_MOUSE
+sp|P08752|GNAI2_MOUSE
diff --git a/txt/value_distribution.png b/txt/value_distribution.png
diff --git a/venn.png b/venn.png