poscon negcon selection experiment by Chloe

[MarziehHaghighi]

Notes from Chloe's emails:

• Email on Aug 19, 2022:

  • For our positive controls, ideally we’d like to establish a reference ORF paired with two mutants, one showing strong shifts and one subtle in the protein channel as well as detectable changes in morphology. In this case, profiling would especially be helpful. For the NegCons, we must slim down our selection to only 4 ORFs – I’m not sure if you guys have preference for selection there.

• Email on Sep 15, 2022:
   

  • Regarding the PosCons, we’d like to select either IMPDH1 or ALK as our reference allele,
    plus two of their respective variants (one which shows strong morphological shifts/localization patterns,
    and one that’s subtle). For NegCons, we can only select 4 to include in our screen –
    I’ll leave it up to you guys which 4 best suit your needs.

  • You can disregard all wells that are not labelled either PosCon or NegCon for this screen.
    And please keep in mind each quadrant received a varying dose of viral supernatant.
    The amount I settled on for our final pipeline is 6 uL, so perhaps you want to pay attention to the wells which received a vTitre = 6.

[MarziehHaghighi]

Transfection threshold selection:

• We don't have untransfected or empty wells as control here. Therefore, I looked at the distribution of all the experiment cells to check for possible patterns.
• Control in the second row plots are negcon which are not necessarily untransfected wells but have more untransfected cells (check if it is True)

• Thresholds for calling a cell untransfected (<0.002) or transfected (>0.01) are fixed based on the previous screen compound screen by Jessie)

Replicate correlations

• All doses combined:

Table

• Different doses as different treatments (a very small subset remained):

Table

Table of values all doses combined

Table

	Variant	RepCor_p	Rand90Perc_p	Rep10Perc_p	RepCor_np	Rand90Perc_np	Rep10Perc_np
0	ACSF3	0.464247	0.242502	0.387773	-0.0876892	0.178258	0.048729
1	ACSF3_PRO243LEU	0.78155	0.242502	0.387773	0.328267	0.178258	0.048729
2	ACY1	0.601593	0.242502	0.387773	0.650239	0.178258	0.048729
3	AGXT_ARG36CYS	0.0265154	0.242502	0.387773	-0.0290838	0.178258	0.048729
4	AGXT_GLY116ARG	0.581136	0.242502	0.387773	0.378216	0.178258	0.048729
5	IMPDH1	0.8263	0.242502	0.387773	0.230296	0.178258	0.048729
6	MAPK13	0.569799	0.242502	0.387773	0.0459195	0.178258	0.048729
7	ACSF3_MET266VAL	0.548294	0.242502	0.387773	0.148804	0.178258	0.048729
8	ACSF3_THR358ILE	0.791574	0.242502	0.387773	0.281238	0.178258	0.048729
9	ADIPOQ	0.378324	0.242502	0.387773	0.153797	0.178258	0.048729
10	AGXT_GLY41ARG	0.46064	0.242502	0.387773	0.198723	0.178258	0.048729
11	AGXT_ARG118CYS	0.760736	0.242502	0.387773	0.252215	0.178258	0.048729
12	IMPDH1_R309P	0.686838	0.242502	0.387773	0.137914	0.178258	0.048729
13	MAPK9	0.868887	0.242502	0.387773	0.589735	0.178258	0.048729
14	ACSF3_GLY119ASP	0.677298	0.242502	0.387773	0.4342	0.178258	0.048729
15	ACSF3_PRO285LEU	0.814984	0.242502	0.387773	0.202351	0.178258	0.048729
16	AGX	0.884426	0.242502	0.387773	0.77108	0.178258	0.048729
17	AGXT_GLY41GLU	0.4088	0.242502	0.387773	-0.0633152	0.178258	0.048729
18	AGXT_ASP129HIS	0.840433	0.242502	0.387773	0.593532	0.178258	0.048729
19	ATG5	0.88402	0.242502	0.387773	0.0805492	0.178258	0.048729
20	PRKACB	0.483937	0.242502	0.387773	-0.110313	0.178258	0.048729
21	ACSF3_ALA197THR	0.718377	0.242502	0.387773	0.255557	0.178258	0.048729
22	ACSF3_GLU359LYS	0.621569	0.242502	0.387773	0.471823	0.178258	0.048729
23	AGXT_MET49LEU	0.767518	0.242502	0.387773	0.625871	0.178258	0.048729
24	AGXT_PHE152ILE	0.769871	0.242502	0.387773	0.169761	0.178258	0.048729
25	IMPDH1_V353I	0.9053	0.242502	0.387773	0.344081	0.178258	0.048729
26	BCL2L1	0.900296	0.242502	0.387773	0.103317	0.178258	0.048729
27	RHEB	0.509347	0.242502	0.387773	0.391508	0.178258	0.048729
28	ACSF3_MET198ARG	0.318605	0.242502	0.387773	0.256162	0.178258	0.048729
29	ACSF3_ARG471TRP	0.636535	0.242502	0.387773	0.406297	0.178258	0.048729
30	AGXT_PRO10AL	0.764129	0.242502	0.387773	0.577206	0.178258	0.048729
31	AGXT_GLY161SER	0.520356	0.242502	0.387773	0.119843	0.178258	0.048729
32	IMPDH1_H457P	0.695327	0.242502	0.387773	-0.0550801	0.178258	0.048729
33	SGK3	0.763358	0.242502	0.387773	0.291186	0.178258	0.048729
34	ACSF3_ILE200ME	0.851562	0.242502	0.387773	0.14699	0.178258	0.048729
35	ACSF3_ARG558TRP	0.807143	0.242502	0.387773	0.33565	0.178258	0.048729
36	AGXT_PRO11HIS	0.493971	0.242502	0.387773	0.528455	0.178258	0.048729
37	AGXT_GLY82ARG	0.871892	0.242502	0.387773	0.818665	0.178258	0.048729
38	ALK	0.90219	0.242502	0.387773	0.419077	0.178258	0.048729
39	SLIRP	0.803155	0.242502	0.387773	0.416025	0.178258	0.048729
40	ACSF3_GLY225ARG	0.667611	0.242502	0.387773	0.438142	0.178258	0.048729
41	ACSF3_ASP457AS	0.386095	0.242502	0.387773	0.0900982	0.178258	0.048729
42	ACTB	0.554377	0.242502	0.387773	0.0740144	0.178258	0.048729
43	AGXT_LYS12ARG	0.373576	0.242502	0.387773	0.269074	0.178258	0.048729
44	AGXT_ALA85ASP	0.653988	0.242502	0.387773	0.111768	0.178258	0.048729
45	RASA1_(ENDO-FREE,_HAND_PREP)_GLU70GLY	0.75082	0.242502	0.387773	0.0762317	0.178258	0.048729
46	STAT1	0.417606	0.242502	0.387773	0.122337	0.178258	0.048729
47	ACTN1	0.758385	0.242502	0.387773	0.258184	0.178258	0.048729
48	AGXT_ASN22SER	0.836479	0.242502	0.387773	0.604089	0.178258	0.048729
49	AGXT_ARG111GL	0.858474	0.242502	0.387773	0.627029	0.178258	0.048729
50	TPM1_(ENDO-FREE,_HAND_PREP)_ASP175AS	0.402873	0.242502	0.387773	0.658127	0.178258	0.048729
51	ALK_R1275Q	0.136352	0.242502	0.387773	0.126207	0.178258	0.048729

Table of values per dose (a very small subset remained)

Table

	Metadata_variant_dose	RepCor_p	Rand90Perc_p	Rep10Perc_p	RepCor_np	Rand90Perc_np	Rep10Perc_np
0	ACSF3_PRO243LEU-18	0.872976	0.574249	0.531375	0.0439548	0.46654	-0.20769
1	ACSF3_PRO243LEU-12	0.760055	0.574249	0.531375	0.144682	0.46654	-0.20769
2	IMPDH1-18	0.693342	0.574249	0.531375	-0.536142	0.46654	-0.20769
3	IMPDH1-12	0.722221	0.574249	0.531375	-0.400952	0.46654	-0.20769
4	ACSF3_PRO243LEU-6	0.826189	0.574249	0.531375	0.599528	0.46654	-0.20769
5	ACSF3_PRO243LEU-3	0.833765	0.574249	0.531375	0.44096	0.46654	-0.20769
6	IMPDH1-6	0.946782	0.574249	0.531375	0.67178	0.46654	-0.20769
7	ACSF3_THR358ILE-18	0.903758	0.574249	0.531375	-0.0572857	0.46654	-0.20769
8	ACSF3_THR358ILE-12	0.844114	0.574249	0.531375	0.731168	0.46654	-0.20769
9	IMPDH1_R309P-18	0.708704	0.574249	0.531375	-0.20769	0.46654	-0.20769
10	IMPDH1_R309P-12	0.878353	0.574249	0.531375	-0.184767	0.46654	-0.20769
11	ACSF3_THR358ILE-6	0.85306	0.574249	0.531375	0.215685	0.46654	-0.20769
12	ACSF3_THR358ILE-3	0.622953	0.574249	0.531375	0.651039	0.46654	-0.20769
13	IMPDH1_R309P-6	0.738742	0.574249	0.531375	0.217266	0.46654	-0.20769
14	IMPDH1_R309P-3	0.689972	0.574249	0.531375	0.24674	0.46654	-0.20769
15	ACSF3_GLU359LYS-12	0.516572	0.574249	0.531375	0.557952	0.46654	-0.20769
16	ACSF3_GLU359LYS-6	0.531375	0.574249	0.531375	0.590245	0.46654	-0.20769
17	ACSF3_GLU359LYS-3	0.661182	0.574249	0.531375	0.385989	0.46654	-0.20769
18	ACSF3_ARG471TRP-18	0.616398	0.574249	0.531375	0.288675	0.46654	-0.20769
19	ACSF3_ARG471TRP-12	0.82272	0.574249	0.531375	0.511135	0.46654	-0.20769
20	ACSF3_ARG471TRP-6	0.274564	0.574249	0.531375	0.135342	0.46654	-0.20769

UMAPs

poscon negcon (protein channel)

plots

poscon - negcon (protein channel)

plots

poscon - negcon (nonprotein channel)

plots

[MarziehHaghighi]

Including untransfected population level profiles

• Untransfected profiles for nonprotein channel are being used for analysis
• Untransfected profiles for protein channel are NOT being used for analysis and are just included for visualization

Positive Controls (ALK and IMPDH1 , 6 uL)

Negative Controls (6 uL)

• (MAPK13, MAPK9, ATG5, PRKACB, BCL2L1, RHEB, CFLAR, SGK3, CLOCK, SLIRP, STAT1, IKBKE, ZBTB24 )

[MarziehHaghighi]

Table of numbers for all doses:

Positive Controls:

plots

	Variant	control_type	vTitre	channel	impact_versus_untransfected	impact_vs_wt
0	IMPDH1	poscon	3	np	0.3	nan
1	IMPDH1_D311	poscon	3	np	nan	nan
2	IMPDH1_H457P	poscon	3	np	0.7	0.68
3	IMPDH1_R309P	poscon	3	np	0.31	0.18
4	IMPDH1_V353I	poscon	3	np	0.24	0.65
5	IMPDH1	poscon	3	p	nan	nan
6	IMPDH1_D311	poscon	3	p	nan	nan
7	IMPDH1_H457P	poscon	3	p	nan	0.91
8	IMPDH1_R309P	poscon	3	p	nan	0.67
9	IMPDH1_V353I	poscon	3	p	nan	0.89
10	ALK	poscon	3	np	0.64	nan
11	ALK_A1234	poscon	3	np	nan	nan
12	ALK_R1275Q	poscon	3	np	nan	nan
13	ALK_T1151M	poscon	3	np	nan	nan
14	ALK	poscon	3	p	nan	nan
15	ALK_A1234	poscon	3	p	nan	nan
16	ALK_R1275Q	poscon	3	p	nan	nan
17	ALK_T1151M	poscon	3	p	nan	nan
18	IMPDH1	poscon	6	np	0.81	nan
19	IMPDH1_D311	poscon	6	np	nan	nan
20	IMPDH1_H457P	poscon	6	np	0.34	0.49
21	IMPDH1_R309P	poscon	6	np	0.17	0.12
22	IMPDH1_V353I	poscon	6	np	0.59	0.85
23	IMPDH1	poscon	6	p	nan	nan
24	IMPDH1_D311	poscon	6	p	nan	nan
25	IMPDH1_H457P	poscon	6	p	nan	0.94
26	IMPDH1_R309P	poscon	6	p	nan	0.57
27	IMPDH1_V353I	poscon	6	p	nan	0.96
28	ALK	poscon	6	np	0.51	nan
29	ALK_A1234	poscon	6	np	nan	nan
30	ALK_F1174L	poscon	6	np	nan	nan
31	ALK_R1275Q	poscon	6	np	0.14	0.08
32	ALK_T1151M	poscon	6	np	0.17	0.03
33	ALK	poscon	6	p	nan	nan
34	ALK_A1234	poscon	6	p	nan	nan
35	ALK_F1174L	poscon	6	p	nan	nan
36	ALK_R1275Q	poscon	6	p	nan	-0.46
37	ALK_T1151M	poscon	6	p	nan	-0.51
38	IMPDH1	poscon	12	np	-0.38	nan
39	IMPDH1_D311	poscon	12	np	nan	nan
40	IMPDH1_H457P	poscon	12	np	nan	0.2
41	IMPDH1_R309P	poscon	12	np	0.23	0.3
42	IMPDH1_V353I	poscon	12	np	0.28	-0.08
43	IMPDH1	poscon	12	p	nan	nan
44	IMPDH1_D311	poscon	12	p	nan	nan
45	IMPDH1_H457P	poscon	12	p	nan	0.81
46	IMPDH1_R309P	poscon	12	p	nan	0.82
47	IMPDH1_V353I	poscon	12	p	nan	0.92
48	ALK	poscon	12	np	0.19	nan
49	ALK_A1234	poscon	12	np	nan	nan
50	ALK_R1275Q	poscon	12	np	nan	nan
51	ALK_T1151M	poscon	12	np	nan	nan
52	ALK	poscon	12	p	nan	nan
53	ALK_A1234	poscon	12	p	nan	nan
54	ALK_R1275Q	poscon	12	p	nan	nan
55	ALK_T1151M	poscon	12	p	nan	nan
56	IMPDH1	poscon	18	np	-0.35	nan
57	IMPDH1_D311	poscon	18	np	nan	nan
58	IMPDH1_H457P	poscon	18	np	nan	0.29
59	IMPDH1_R309P	poscon	18	np	-0	-0.1
60	IMPDH1_V353I	poscon	18	np	0.43	0.05
61	IMPDH1	poscon	18	p	nan	nan
62	IMPDH1_D311	poscon	18	p	nan	nan
63	IMPDH1_H457P	poscon	18	p	nan	0.79
64	IMPDH1_R309P	poscon	18	p	nan	0.86
65	IMPDH1_V353I	poscon	18	p	nan	0.91
66	ALK	poscon	18	np	nan	nan
67	ALK_F1174L	poscon	18	np	nan	nan
68	ALK_R1275Q	poscon	18	np	0.26	0.54
69	ALK_T1151M	poscon	18	np	nan	nan
70	ALK	poscon	18	p	nan	nan
71	ALK_F1174L	poscon	18	p	nan	nan
72	ALK_R1275Q	poscon	18	p	nan	-0.18
73	ALK_T1151M	poscon	18	p	nan	nan

Negative Controls:

Table

	Variant	control_type	vTitre	channel	impact_versus_untransfected
0	MAPK13	negcon	3	np	0.17
1	MAPK9	negcon	3	np	0.73
2	ATG5	negcon	3	np	0.29
3	PRKACB	negcon	3	np	0.28
4	BCL2L1	negcon	3	np	0.38
5	RHEB	negcon	3	np	0.63
6	CFLAR	negcon	3	np	nan
7	SGK3	negcon	3	np	0.34
8	CLOCK	negcon	3	np	nan
9	SLIRP	negcon	3	np	0.48
10	STAT1	negcon	3	np	0.84
11	IKBKE	negcon	3	np	nan
12	ZBTB24	negcon	3	np	nan
13	MAPK13	negcon	3	p	nan
14	MAPK9	negcon	3	p	nan
15	ATG5	negcon	3	p	nan
16	PRKACB	negcon	3	p	nan
17	BCL2L1	negcon	3	p	nan
18	RHEB	negcon	3	p	nan
19	CFLAR	negcon	3	p	nan
20	SGK3	negcon	3	p	nan
21	CLOCK	negcon	3	p	nan
22	SLIRP	negcon	3	p	nan
23	STAT1	negcon	3	p	nan
24	IKBKE	negcon	3	p	nan
25	ZBTB24	negcon	3	p	nan
26	MAPK13	negcon	6	np	nan
27	MAPK9	negcon	6	np	0.52
28	ATG5	negcon	6	np	0.63
29	PRKACB	negcon	6	np	0.9
30	BCL2L1	negcon	6	np	0.28
31	RHEB	negcon	6	np	0.42
32	CFLAR	negcon	6	np	nan
33	SGK3	negcon	6	np	-0.07
34	CLOCK	negcon	6	np	nan
35	SLIRP	negcon	6	np	0.81
36	STAT1	negcon	6	np	0.51
37	IKBKE	negcon	6	np	nan
38	ZBTB24	negcon	6	np	nan
39	MAPK13	negcon	6	p	nan
40	MAPK9	negcon	6	p	nan
41	ATG5	negcon	6	p	nan
42	PRKACB	negcon	6	p	nan
43	BCL2L1	negcon	6	p	nan
44	RHEB	negcon	6	p	nan
45	CFLAR	negcon	6	p	nan
46	SGK3	negcon	6	p	nan
47	CLOCK	negcon	6	p	nan
48	SLIRP	negcon	6	p	nan
49	STAT1	negcon	6	p	nan
50	IKBKE	negcon	6	p	nan
51	ZBTB24	negcon	6	p	nan
52	MAPK13	negcon	12	np	0.42
53	MAPK9	negcon	12	np	0.62
54	ATG5	negcon	12	np	nan
55	PRKACB	negcon	12	np	0.27
56	BCL2L1	negcon	12	np	0.59
57	RHEB	negcon	12	np	0.54
58	CFLAR	negcon	12	np	0.3
59	SGK3	negcon	12	np	0.43
60	CLOCK	negcon	12	np	nan
61	SLIRP	negcon	12	np	0.58
62	STAT1	negcon	12	np	-0.25
63	IKBKE	negcon	12	np	nan
64	ZBTB24	negcon	12	np	nan
65	MAPK13	negcon	12	p	nan
66	MAPK9	negcon	12	p	nan
67	ATG5	negcon	12	p	nan
68	PRKACB	negcon	12	p	nan
69	BCL2L1	negcon	12	p	nan
70	RHEB	negcon	12	p	nan
71	CFLAR	negcon	12	p	nan
72	SGK3	negcon	12	p	nan
73	CLOCK	negcon	12	p	nan
74	SLIRP	negcon	12	p	nan
75	STAT1	negcon	12	p	nan
76	IKBKE	negcon	12	p	nan
77	ZBTB24	negcon	12	p	nan
78	MAPK9	negcon	18	np	0.66
79	ATG5	negcon	18	np	0.5
80	PRKACB	negcon	18	np	0.2
81	BCL2L1	negcon	18	np	0.49
82	RHEB	negcon	18	np	0.54
83	CFLAR	negcon	18	np	nan
84	SGK3	negcon	18	np	nan
85	CLOCK	negcon	18	np	nan
86	SLIRP	negcon	18	np	0.08
87	STAT1	negcon	18	np	nan
88	IKBKE	negcon	18	np	nan
89	ZBTB24	negcon	18	np	nan
90	MAPK9	negcon	18	p	nan
91	ATG5	negcon	18	p	nan
92	PRKACB	negcon	18	p	nan
93	BCL2L1	negcon	18	p	nan
94	RHEB	negcon	18	p	nan
95	CFLAR	negcon	18	p	nan
96	SGK3	negcon	18	p	nan
97	CLOCK	negcon	18	p	nan
98	SLIRP	negcon	18	p	nan
99	STAT1	negcon	18	p	nan
100	IKBKE	negcon	18	p	nan
101	ZBTB24	negcon	18	p	nan

[MarziehHaghighi]

My Observations:

Positive controls:

• ALK shows

  • Morphological changes in non-protein channels after transfection for both WT and Mutants (those passing the level of transfection efficiency)
  • Strong protein channel changes for two of its variants: ALK_R1275Q and ALK_T1151M
  • The rest of it variants have a very low transfection efficiency

• IMPDH1 shows

  • Morphological changes in non-protein channels just for a subset of its variants
  • Subtle protein channel changes for just on of its variant IMPDH1_R309P (it has low replicate correlation though)
  • The rest of it variants have a very low transfection efficiency or no signature in the protein channel
  • The observation holds for all the doses

Negative controls:

• CFLAR, IKBKE , CLOCK, MAPK13 and ZBTB24 show
  • a very low transfection efficiency.
• SGK3 and BCL2L1 show
  • Strong morphological changes in non-protein channels after transfection
• RHEB and MAPK9 and STAT1 show
  • High transfection efficiency and mild changes in the nonprotein channel
• PRKACB and SLIRP show
  • Medium transfection efficiency and vey minor changes in the nonprotein channel

[MarziehHaghighi]

@AnneCarpenter the context of this experiment is selection of positive and negative controls based on what we recommended in #1

[renochlo]

• We don't have untransfected or empty wells as control here

There are un-transduced, empty wells where cells should not have survived selection in columns 19-24. Sorry if that was unclear. Also how are you calling cells 'untransfected'? Is that based on low GFP intensity? All wells (except col19-24) were transduced with GFP and puro resistance. Therefore, following selection, all cells should be transduced. Cells with low GFP intensity in this screen should then reflect low protein stability.

[MarziehHaghighi]

Thanks for the note @renochlo . The preprocessed CellProfiler single cell extracted features I have access to are for row A to P and columns 1 to 18. Also, I usually start with the metadata notes to decide on analysis choices and there were no notes on controls for this experiment. For transfection efficacy, I followed the our routine for this analysis which is first detecting transfected cells (based on DsRed or protein channel - this time the name was GFP in the feature names) and limit the computational scoring in the protein channel to the transfected cells. Are you saying that for this batch we consider all cells to be transducted and we want to include all in the analysis?

[renochlo]

I see, I'll be sure to include that in the future then. The plan moving forward is to include one control (4x wells/plate) that will not be transduced and therefore all cells should round up/undergo apoptosis. And that's correct - all cells should be treated as transduced and therefore included.

[MarziehHaghighi]

With the assumption mentioned above there is not much analysis to do on data, negcon doesn't have replicate. For the subset of data with replicates, below are the replicate correlation curves. The replicate correlation with the transfected untrasfected assumption was stronger which means a potential relationship between protein abundance and phenotype strength.

Table of numbers for all doses and variants in the experiment:

columns:
Metadata_Sample_Unique: variant
cc_p: correlation coefficient with its wild-type in protein channel
cc_np: correlation coefficient with its wild-type in non-protein channels
RepCor_p,RepCor_np: replicate correlations for protein and non-protein channels

Table

	Metadata_Sample_Unique	cc_p	Gene-dose	wt_RepCor_p	cc_np	wt_RepCor_np	RepCor_p	Rand90Perc_p	Rep10Perc_p	RepCor_np	Rand90Perc_np	Rep10Perc_np
0	ALK F1174L-18	-0.753374	ALK-18	nan	-0.147045	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
1	ALK R1275Q-18	-0.763229	ALK-18	nan	-0.0754998	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
2	ALK T1151M-18	-0.79673	ALK-18	nan	-0.258066	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
3	ALK A1234-12	-0.612243	ALK-12	nan	-0.0686385	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
4	ALK F1174L-12	-0.639578	ALK-12	nan	-0.236033	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
5	ALK R1275Q-12	-0.762841	ALK-12	nan	-0.325995	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
6	ALK T1151M-12	-0.773747	ALK-12	nan	-0.309328	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
7	ACSF3 ALA197THR-18	-0.299739	ACSF3-18	nan	0.215053	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
8	ACSF3 ARG10TRP-18	0.477977	ACSF3-18	nan	-0.356891	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
9	ACSF3 ARG471TRP-18	-0.0441389	ACSF3-18	nan	-0.206069	nan	-0.296662	0.722659	0.0868252	0.23745	0.518714	0.240371
10	ACSF3 ARG558TRP-18	-0.172124	ACSF3-18	nan	0.0455712	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
11	ACSF3 ASP457AS-18	-0.20514	ACSF3-18	nan	-0.450487	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
12	ACSF3 GLU359LYS-18	0.278751	ACSF3-18	nan	0.185034	nan	0.321108	0.722659	0.0868252	0.32855	0.518714	0.240371
13	ACSF3 GLY119ASP-18	-0.357734	ACSF3-18	nan	-0.435534	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
14	ACSF3 GLY225ARG-18	-0.00369709	ACSF3-18	nan	-0.445778	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
15	ACSF3 ILE200ME-18	-0.416649	ACSF3-18	nan	-0.48133	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
16	ACSF3 MET198ARG-18	-0.126327	ACSF3-18	nan	0.442392	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
17	ACSF3 MET266VAL-18	-0.12838	ACSF3-18	nan	-0.412496	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
18	ACSF3 PRO243LEU-18	-0.0807013	ACSF3-18	nan	0.314434	nan	0.79559	0.722659	0.0868252	0.388187	0.518714	0.240371
19	ACSF3 PRO285LEU-18	-0.422939	ACSF3-18	nan	-0.0189845	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
20	ACSF3 SER431TYR-18	0.450857	ACSF3-18	nan	-0.428843	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
21	ACSF3 THR358ILE-18	-0.217192	ACSF3-18	nan	-0.499467	nan	0.953483	0.722659	0.0868252	0.715713	0.518714	0.240371
22	ALK A1234-6	-0.820451	ALK-6	nan	-0.0139152	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
23	ALK F1174L-6	-0.793734	ALK-6	nan	-0.247326	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
24	ALK R1275Q-6	-0.763686	ALK-6	nan	-0.317256	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
25	ALK T1151M-6	-0.704172	ALK-6	nan	-0.030251	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
26	ACSF3 ALA197THR-3	-0.120288	ACSF3-3	nan	0.0694537	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
27	ACSF3 ARG10TRP-3	0.892355	ACSF3-3	nan	0.548597	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
28	ACSF3 ARG471TRP-3	0.327186	ACSF3-3	nan	0.0768689	nan	0.0669798	0.722659	0.0868252	0.633465	0.518714	0.240371
29	ACSF3 ARG558TRP-3	0.320104	ACSF3-3	nan	0.232489	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
30	ACSF3 ASP457AS-3	0.758579	ACSF3-3	nan	-0.10832	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
31	ACSF3 GLU359LYS-3	0.197972	ACSF3-3	nan	0.0651883	nan	0.632249	0.722659	0.0868252	0.489962	0.518714	0.240371
32	ACSF3 GLY119ASP-3	0.387582	ACSF3-3	nan	0.0859518	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
33	ACSF3 GLY225ARG-3	0.521877	ACSF3-3	nan	0.156464	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
34	ACSF3 ILE200ME-3	0.52762	ACSF3-3	nan	-0.150466	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
35	ACSF3 MET198ARG-3	0.526373	ACSF3-3	nan	0.033568	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
36	ACSF3 MET266VAL-3	0.637319	ACSF3-3	nan	0.013707	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
37	ACSF3 PRO243LEU-3	0.148243	ACSF3-3	nan	0.0619215	nan	0.410711	0.722659	0.0868252	0.61891	0.518714	0.240371
38	ACSF3 PRO285LEU-3	-0.574455	ACSF3-3	nan	-0.0690662	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
39	ACSF3 SER431TYR-3	0.913414	ACSF3-3	nan	0.768222	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
40	ACSF3 THR358ILE-3	0.40817	ACSF3-3	nan	0.120126	nan	0.755309	0.722659	0.0868252	0.836975	0.518714	0.240371
41	IMPDH1 D311-12	-0.774849	IMPDH1-12	0.760764	-0.460879	0.36131	nan	0.722659	0.0868252	nan	0.518714	0.240371
42	IMPDH1 H457P-12	0.817813	IMPDH1-12	0.760764	0.777185	0.36131	nan	0.722659	0.0868252	nan	0.518714	0.240371
43	IMPDH1 R309P-12	0.847418	IMPDH1-12	0.760764	0.731387	0.36131	0.899226	0.722659	0.0868252	0.516074	0.518714	0.240371
44	IMPDH1 V353I-12	0.935036	IMPDH1-12	0.760764	0.768386	0.36131	nan	0.722659	0.0868252	nan	0.518714	0.240371
45	ACSF3 ALA197THR-6	-0.326597	ACSF3-6	nan	-0.0177196	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
46	ACSF3 ARG10TRP-6	-0.126838	ACSF3-6	nan	0.36074	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
47	ACSF3 ARG471TRP-6	-0.425151	ACSF3-6	nan	-0.270017	nan	-0.00870186	0.722659	0.0868252	0.0872559	0.518714	0.240371
48	ACSF3 ARG558TRP-6	-0.460639	ACSF3-6	nan	-0.260127	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
49	ACSF3 ASP457AS-6	-0.222509	ACSF3-6	nan	0.390782	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
50	ACSF3 GLU359LYS-6	-0.421248	ACSF3-6	nan	-0.493276	nan	0.799983	0.722659	0.0868252	0.404573	0.518714	0.240371
51	ACSF3 GLY119ASP-6	-0.436885	ACSF3-6	nan	-0.347228	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
52	ACSF3 GLY225ARG-6	-0.34149	ACSF3-6	nan	-0.569767	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
53	ACSF3 ILE200ME-6	-0.430521	ACSF3-6	nan	-0.107794	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
54	ACSF3 MET198ARG-6	-0.479049	ACSF3-6	nan	0.172184	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
55	ACSF3 MET266VAL-6	-0.439538	ACSF3-6	nan	-0.24091	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
56	ACSF3 PRO243LEU-6	-0.361676	ACSF3-6	nan	0.0219164	nan	0.510791	0.722659	0.0868252	0.662999	0.518714	0.240371
57	ACSF3 PRO285LEU-6	-0.327249	ACSF3-6	nan	0.0476871	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
58	ACSF3 SER431TYR-6	-0.133967	ACSF3-6	nan	-0.189617	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
59	ACSF3 THR358ILE-6	-0.467527	ACSF3-6	nan	-0.297932	nan	0.885713	0.722659	0.0868252	0.639241	0.518714	0.240371
60	IMPDH1 D311-6	-0.851162	IMPDH1-6	0.956671	-0.283756	0.817855	nan	0.722659	0.0868252	nan	0.518714	0.240371
61	IMPDH1 H457P-6	0.963299	IMPDH1-6	0.956671	0.821758	0.817855	nan	0.722659	0.0868252	nan	0.518714	0.240371
62	IMPDH1 R309P-6	0.840769	IMPDH1-6	0.956671	0.632619	0.817855	0.91883	0.722659	0.0868252	0.466657	0.518714	0.240371
63	IMPDH1 V353I-6	0.971243	IMPDH1-6	0.956671	0.941578	0.817855	nan	0.722659	0.0868252	nan	0.518714	0.240371
64	ALK A1234-3	-0.801285	ALK-3	nan	-0.178994	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
65	ALK F1174L-3	-0.460542	ALK-3	nan	-0.152737	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
66	ALK R1275Q-3	-0.751943	ALK-3	nan	-0.159105	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
67	ALK T1151M-3	-0.533459	ALK-3	nan	0.0589959	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
68	ACSF3 ALA197THR-12	-0.0128909	ACSF3-12	nan	0.122684	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
69	ACSF3 ARG10TRP-12	-0.0964737	ACSF3-12	nan	-0.348165	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
70	ACSF3 ARG471TRP-12	-0.231174	ACSF3-12	nan	-0.269564	nan	0.27248	0.722659	0.0868252	0.554462	0.518714	0.240371
71	ACSF3 ARG558TRP-12	-0.0751835	ACSF3-12	nan	0.0348755	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
72	ACSF3 ASP457AS-12	-0.270994	ACSF3-12	nan	-0.146944	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
73	ACSF3 GLU359LYS-12	0.0437622	ACSF3-12	nan	0.231162	nan	0.166207	0.722659	0.0868252	0.526845	0.518714	0.240371
74	ACSF3 GLY119ASP-12	-0.17127	ACSF3-12	nan	-0.3923	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
75	ACSF3 GLY225ARG-12	-0.171017	ACSF3-12	nan	-0.414685	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
76	ACSF3 ILE200ME-12	-0.2832	ACSF3-12	nan	-0.28015	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
77	ACSF3 MET198ARG-12	0.158229	ACSF3-12	nan	0.219664	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
78	ACSF3 MET266VAL-12	-0.0700601	ACSF3-12	nan	-0.0183695	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
79	ACSF3 PRO243LEU-12	-0.111264	ACSF3-12	nan	-0.050846	nan	0.565464	0.722659	0.0868252	0.252055	0.518714	0.240371
80	ACSF3 PRO285LEU-12	-0.0266271	ACSF3-12	nan	0.069777	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
81	ACSF3 SER431TYR-12	-0.108681	ACSF3-12	nan	-0.309151	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
82	ACSF3 THR358ILE-12	-0.163059	ACSF3-12	nan	-0.242129	nan	0.937996	0.722659	0.0868252	0.828318	0.518714	0.240371
83	IMPDH1 D311-3	-0.856673	IMPDH1-3	nan	-0.356465	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
84	IMPDH1 H457P-3	0.933294	IMPDH1-3	nan	0.89243	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
85	IMPDH1 R309P-3	0.855226	IMPDH1-3	nan	0.625438	nan	0.919534	0.722659	0.0868252	0.60304	0.518714	0.240371
86	IMPDH1 V353I-3	0.93677	IMPDH1-3	nan	0.865481	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
87	IMPDH1 D311-18	-0.853111	IMPDH1-18	0.740127	-0.371824	-0.00425384	nan	0.722659	0.0868252	nan	0.518714	0.240371
88	IMPDH1 H457P-18	0.880043	IMPDH1-18	0.740127	0.571542	-0.00425384	nan	0.722659	0.0868252	nan	0.518714	0.240371
89	IMPDH1 R309P-18	0.910156	IMPDH1-18	0.740127	0.508082	-0.00425384	0.836808	0.722659	0.0868252	0.341252	0.518714	0.240371
90	IMPDH1 V353I-18	0.91595	IMPDH1-18	0.740127	0.724903	-0.00425384	nan	0.722659	0.0868252	nan	0.518714	0.240371

Positive Controls - dose 6:

Table

Metadata_Sample_Unique	cc_p	Gene-dose	wt_RepCor_p	cc_np	wt_RepCor_np	RepCor_p	Rand90Perc_p	Rep10Perc_p	RepCor_np	Rand90Perc_np	Rep10Perc_np
ALK A1234-6	-0.820451	ALK-6	nan	-0.0139152	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
ALK F1174L-6	-0.793734	ALK-6	nan	-0.247326	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
ALK R1275Q-6	-0.763686	ALK-6	nan	-0.317256	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
ALK T1151M-6	-0.704172	ALK-6	nan	-0.030251	nan	nan	0.722659	0.0868252	nan	0.518714	0.240371
IMPDH1 D311-6	-0.851162	IMPDH1-6	0.956671	-0.283756	0.817855	nan	0.722659	0.0868252	nan	0.518714	0.240371
IMPDH1 H457P-6	0.963299	IMPDH1-6	0.956671	0.821758	0.817855	nan	0.722659	0.0868252	nan	0.518714	0.240371
IMPDH1 R309P-6	0.840769	IMPDH1-6	0.956671	0.632619	0.817855	0.91883	0.722659	0.0868252	0.466657	0.518714	0.240371
IMPDH1 V353I-6	0.971243	IMPDH1-6	0.956671	0.941578	0.817855	nan	0.722659	0.0868252	nan	0.518714	0.240371

Negative Controls - dose 6:

• For negative controls the group uses replicate correlations as the proxy for showing a signature which in this dataset we dont have access to (each dose for negcon have just one well). In general I'm opposed to that assumption but we dont have replicates here anyways.