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 Rv1141c/echA11:

update plot	correlation	link to info on gene
Rv1526c/-	(cc=0.5088)	info on Rv1526c/-
Rv2425c/-	(cc=0.488)	info on Rv2425c/-
Rv3016/lpqA	(cc=0.4866)	info on Rv3016/lpqA
Rv1787/PPE25	(cc=0.4835)	info on Rv1787/PPE25
Rv2147c/-	(cc=0.4766)	info on Rv2147c/-
Rv2345/-	(cc=0.4695)	info on Rv2345/-
Rv3190A/-	(cc=0.4649)	info on Rv3190A/-
Rv1000c/-	(cc=0.4537)	info on Rv1000c/-
Rv1981c/nrdF1	(cc=0.4511)	info on Rv1981c/nrdF1
Rv2300c/-	(cc=0.4476)	info on Rv2300c/-

Correlation of Rv1141c/echA11 with Rv3190A/-

Normalized LFCs for Rv1141c/echA11:
(description and provenance of datasets)

	Rv1141c/echA11	Rv3190A/-
Fe_supp_jason_reseq	-1.143	-0.586
low_pH_jason_reseq	-1.589	-2.028
NO_jason_reseq	0.365	0.625
B6_jason_reseq	-0.567	-1.103
MHCII_jason_reseq	-0.357	-0.835
Isoniazid02	-0.201	0.578
Rifampicin4	0.872	-0.352
Ethambutol3	-0.078	1.811
Meropenem3	0.399	1.127
Vancomycin16	-0.151	0.427
Rv2680_day32	-0.615	-0.28
H37Rv_KO_MarP	0.072	0.119
hypoxia_3wks	-0.148	-0.271
hypoxia_6wks	0.104	0.305
glycerol	0.478	0.039
cholesterol	-0.485	-1.12
AJ	0.121	0.734
Bibs02	-0.152	-0.029
Bibs02c	1.144	-0.076
BL6	0.694	0.34
BL6a	1.115	0.616
BXD01	0.577	0.217
BXD010	0.13	1.089
BXD011	2.406	0.536
BXD03	0.515	-0.281
BXD04	0.477	-0.245
BXD05	-0.083	0.188
BXD06	0.221	0.139
BXD07	0.805	0.074
BXD08	0.228	0.539
BXD09	0.496	0.855
CAST	0.582	0.674
CCcont	0.401	0.667
DS01	-0.031	-0.144
DS02	-0.244	0.551
DS04	0.013	-1.189
DS0c	0.057	0.181
GP01	1.232	0.519
GP02	0.471	-0.768
GP0c	0.902	0.247
NOD	0.496	1.601
NZO	-0.361	-0.088
PWK	0.423	0.352
H37Rv_KO_CtpC	0.81	1.212
H37Rv_KO_CtpD	1.174	0.503
H37Rv_KO_Rv1272	0.686	0.0
H37Rv_KO_SugABC	1.109	0.26
H37Rv_KO_MbtN	0.806	0.07
Trans05	0.467	-0.685
macrophage_unactivated	0.363	0.335
IL1	0.163	0.593
Rapamycin	0.129	-0.35
Tcell	0.837	-0.042
GMCSF	0.977	0.438
IFNab	0.021	-0.995
IFNg	-0.115	0.171
IFNg_GMCSF1	0.955	-0.779
Rv1432_day32	-0.292	-0.05
Rv1565c_day32	0.325	-0.477
secA2_input	-0.063	-0.833
delta_Rv3594	0.285	0.679
delta_Rv3717	0.159	0.949
delta_Rv3811	0.7	0.943
delta_Rv0954	0.424	0.136
PonA1	-0.504	0.201
EccD1_KO	1.5	1.02
EspI_KO	1.483	0.884
PE35_KO	0.718	1.663
PPE68_KO	1.488	1.709
glycerol2	0.921	1.087
lignocerate	1.108	1.478
oleate	1.231	0.194
phosphatidylcholine	1.325	1.106
acetate	0.545	1.122
glucAc	0.461	1.216
Rv0950ko	-0.353	1.282
Rv1096ko	0.103	0.498
Rv3684ko	-0.508	-0.111
delta_otsA_trehalose	1.225	1.294