TnSeqCorr

• These are correlations of TnSeq responses across 82 experimental conditions.
• LFCs (log2-fold-changes) were computed for each gene in each condition relative to a relevant control condition (e.g. H37Rv grown on 7H9).
• The LFCs were normalized by dividing by the standard deviation for each condition. (so roughly, |LFC|>2 are the outliers, i.e. tails of the distribution)
• Note that essential genes often have LFCs around 0.
• Data for some genes is not available if they have less than 3 TA sites, or the dynamic range of LFCs is less than 2.0 across all conditions. (This is the case for many essential genes.)
• 'leverage' on each plot is a statistical score that indicates how much the regression is influenced by a few outlier points; the traditional threshold is indicated on the plots (3p/n, which is about 0.07 for this dataset), but in practice, cases with leverage > ~0.2 seem to be the least reliable (most misleading) correlation coefficients.

Top 10 genes with highest correlation to Rv1013/pks16:

update plot	correlation	link to info on gene
Rv1366/-	(cc=0.5409)	info on Rv1366/-
Rv0072/-	(cc=0.5362)	info on Rv0072/-
Rv0643c/mmaA3	(cc=0.5343)	info on Rv0643c/mmaA3
Rv2777c/-	(cc=0.5297)	info on Rv2777c/-
Rv3823c/mmpL8	(cc=0.5196)	info on Rv3823c/mmpL8
Rv0235c/-	(cc=0.5066)	info on Rv0235c/-
Rv3555c/-	(cc=0.494)	info on Rv3555c/-
Rv2444c/rne	(cc=0.4901)	info on Rv2444c/rne
Rv3148/nuoD	(cc=0.4812)	info on Rv3148/nuoD
Rv3421c/-	(cc=0.4794)	info on Rv3421c/-

Correlation of Rv1013/pks16 with Rv0072/-

Normalized LFCs for Rv1013/pks16:
(description and provenance of datasets)

	Rv1013/pks16	Rv0072/-
Fe_supp_jason_reseq	0.48	-0.362
low_pH_jason_reseq	-0.495	-0.049
NO_jason_reseq	1.533	0.0
B6_jason_reseq	-1.271	-0.064
MHCII_jason_reseq	-3.023	-0.69
Isoniazid02	-1.756	-1.484
Rifampicin4	0.019	0.225
Ethambutol3	2.037	1.0
Meropenem3	1.0	0.265
Vancomycin16	-0.236	-1.013
Rv2680_day32	-0.362	-0.869
H37Rv_KO_MarP	0.968	0.49
hypoxia_3wks	-3.334	-0.546
hypoxia_6wks	-3.909	-0.194
glycerol	-0.856	-0.279
cholesterol	-1.194	0.012
AJ	0.435	0.24
Bibs02	-0.029	0.84
Bibs02c	-1.15	0.791
BL6	1.133	0.855
BL6a	0.319	0.816
BXD01	0.994	0.493
BXD010	2.464	0.642
BXD011	1.442	0.508
BXD03	2.47	0.366
BXD04	1.886	0.45
BXD05	1.862	0.87
BXD06	1.863	0.744
BXD07	1.419	0.723
BXD08	1.095	0.582
BXD09	2.209	0.086
CAST	0.0	0.47
CCcont	2.434	0.543
DS01	-0.636	1.047
DS02	-0.106	-0.112
DS04	0.561	1.737
DS0c	0.919	0.559
GP01	2.567	0.569
GP02	2.671	0.645
GP0c	1.142	0.418
NOD	-0.185	0.111
NZO	-0.342	-0.354
PWK	1.903	0.539
H37Rv_KO_CtpC	1.227	0.552
H37Rv_KO_CtpD	0.133	1.424
H37Rv_KO_Rv1272	0.656	1.122
H37Rv_KO_SugABC	-0.099	0.979
H37Rv_KO_MbtN	1.591	0.703
Trans05	0.998	1.394
macrophage_unactivated	-0.552	0.114
IL1	-0.917	0.119
Rapamycin	-0.853	-0.043
Tcell	0.984	0.489
GMCSF	-1.941	-0.388
IFNab	-2.065	0.16
IFNg	-2.539	0.246
IFNg_GMCSF1	-2.212	-0.145
Rv1432_day32	0.463	0.263
Rv1565c_day32	1.501	0.896
secA2_input	-2.481	-0.762
delta_Rv3594	-1.239	-0.174
delta_Rv3717	0.375	-0.366
delta_Rv3811	-2.174	-0.277
delta_Rv0954	0.823	-0.674
PonA1	0.768	0.005
EccD1_KO	-0.191	-0.391
EspI_KO	0.128	-0.094
PE35_KO	-1.068	-0.335
PPE68_KO	-0.218	-0.259
glycerol2	-0.073	1.003
lignocerate	4.396	1.056
oleate	6.0	1.041
phosphatidylcholine	2.531	0.473
acetate	1.438	0.336
glucAc	0.923	0.188
Rv0950ko	-0.956	0.078
Rv1096ko	-0.323	-0.181
Rv3684ko	1.166	-0.468
delta_otsA_trehalose	-0.506	-0.703