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 Rv1588c/-:

update plot	correlation	link to info on gene
Rv3466/-	(cc=0.9134)	info on Rv3466/-
Rv0094c/-	(cc=0.7449)	info on Rv0094c/-
Rv3467/-	(cc=0.7169)	info on Rv3467/-
Rv1756c/-	(cc=0.6019)	info on Rv1756c/-
Rv3475/-	(cc=0.601)	info on Rv3475/-
Rv1369c/-	(cc=0.5964)	info on Rv1369c/-
Rv3380c/-	(cc=0.5913)	info on Rv3380c/-
Rv1764/-	(cc=0.5883)	info on Rv1764/-
Rv2649/-	(cc=0.587)	info on Rv2649/-
Rv3326/-	(cc=0.5867)	info on Rv3326/-

Correlation of Rv1588c/- with Rv2649/-

Normalized LFCs for Rv1588c/-:
(description and provenance of datasets)

	Rv1588c/-	Rv2649/-
Fe_supp_jason_reseq	0.204	-0.259
low_pH_jason_reseq	-0.211	-0.333
NO_jason_reseq	0.412	0.236
B6_jason_reseq	-0.14	-0.422
MHCII_jason_reseq	-0.465	0.0
Isoniazid02	0.566	0.057
Rifampicin4	0.593	1.075
Ethambutol3	0.123	0.612
Meropenem3	-0.097	-0.132
Vancomycin16	0.459	0.088
Rv2680_day32	-1.031	0.169
H37Rv_KO_MarP	-0.042	-0.157
hypoxia_3wks	-0.247	0.431
hypoxia_6wks	-0.712	0.077
glycerol	-0.585	-0.635
cholesterol	-0.622	0.144
AJ	-0.025	1.351
Bibs02	1.02	1.125
Bibs02c	0.617	1.814
BL6	-0.476	0.029
BL6a	0.449	0.911
BXD01	0.307	0.613
BXD010	-0.197	0.729
BXD011	-0.68	0.75
BXD03	0.444	0.661
BXD04	0.334	0.473
BXD05	0.029	0.959
BXD06	-0.091	0.423
BXD07	0.251	0.702
BXD08	0.241	0.433
BXD09	0.133	0.667
CAST	0.1	1.303
CCcont	-0.433	0.009
DS01	1.095	1.042
DS02	1.268	0.901
DS04	0.871	1.143
DS0c	0.863	1.122
GP01	0.37	1.149
GP02	0.734	1.403
GP0c	0.593	0.705
NOD	-0.618	1.256
NZO	-0.09	1.019
PWK	0.705	1.162
H37Rv_KO_CtpC	0.634	0.771
H37Rv_KO_CtpD	-0.876	0.903
H37Rv_KO_Rv1272	0.031	0.47
H37Rv_KO_SugABC	-1.193	0.757
H37Rv_KO_MbtN	-0.758	0.647
Trans05	0.407	0.804
macrophage_unactivated	-0.739	-0.865
IL1	-0.825	-0.365
Rapamycin	-0.988	-0.466
Tcell	-1.199	-1.268
GMCSF	-0.734	-0.269
IFNab	-0.52	-0.707
IFNg	-0.984	-0.347
IFNg_GMCSF1	0.327	-0.148
Rv1432_day32	-0.117	0.533
Rv1565c_day32	0.256	0.13
secA2_input	0.877	-0.337
delta_Rv3594	-0.535	-0.121
delta_Rv3717	-0.586	-0.111
delta_Rv3811	-1.21	-0.064
delta_Rv0954	-0.204	0.457
PonA1	-0.422	0.0
EccD1_KO	0.572	0.099
EspI_KO	1.021	0.858
PE35_KO	0.263	0.75
PPE68_KO	0.813	0.33
glycerol2	-1.265	-0.954
lignocerate	-0.884	-0.756
oleate	-1.221	-1.069
phosphatidylcholine	-1.069	-0.828
acetate	0.441	-0.329
glucAc	-0.011	-0.013
Rv0950ko	-0.678	-0.148
Rv1096ko	0.103	0.06
Rv3684ko	-0.671	-0.599
delta_otsA_trehalose	0.576	0.193