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 Rv1260/-:

update plot	correlation	link to info on gene
Rv0755c/PPE12	(cc=0.602)	info on Rv0755c/PPE12
Rv1646/PE17	(cc=0.5383)	info on Rv1646/PE17
Rv2808/-	(cc=0.5176)	info on Rv2808/-
Rv0669c/-	(cc=0.5018)	info on Rv0669c/-
Rv3784/-	(cc=0.486)	info on Rv3784/-
Rv1087/PE_PGRS21	(cc=0.4856)	info on Rv1087/PE_PGRS21
Rv1378c/-	(cc=0.4856)	info on Rv1378c/-
Rv3697c/vapC48	(cc=0.4849)	info on Rv3697c/vapC48
Rv0739/-	(cc=0.4837)	info on Rv0739/-
Rv1818c/PE_PGRS33	(cc=0.4818)	info on Rv1818c/PE_PGRS33

Correlation of Rv1260/- with Rv3784/-

Normalized LFCs for Rv1260/-:
(description and provenance of datasets)

	Rv1260/-	Rv3784/-
Fe_supp_jason_reseq	-1.051	0.006
low_pH_jason_reseq	-0.555	-0.898
NO_jason_reseq	-0.743	-0.21
B6_jason_reseq	0.641	0.092
MHCII_jason_reseq	0.565	0.297
Isoniazid02	0.247	0.688
Rifampicin4	-0.141	-0.138
Ethambutol3	-0.032	1.0
Meropenem3	0.0	0.948
Vancomycin16	-0.138	0.066
Rv2680_day32	-0.597	0.337
H37Rv_KO_MarP	-0.214	0.03
hypoxia_3wks	0.0	-0.04
hypoxia_6wks	0.148	0.092
glycerol	0.607	0.522
cholesterol	0.847	0.186
AJ	0.225	0.546
Bibs02	0.758	0.0
Bibs02c	0.674	0.588
BL6	-1.235	0.22
BL6a	0.165	0.455
BXD01	0.074	0.05
BXD010	0.717	0.168
BXD011	0.437	0.112
BXD03	-0.573	-0.091
BXD04	-0.194	0.291
BXD05	-0.08	-0.244
BXD06	-0.209	0.22
BXD07	-0.082	-0.032
BXD08	-0.277	0.132
BXD09	-0.062	0.236
CAST	0.484	0.506
CCcont	-0.209	0.043
DS01	0.785	0.185
DS02	0.857	0.495
DS04	0.475	-0.07
DS0c	0.767	0.176
GP01	-1.091	0.273
GP02	0.286	0.114
GP0c	-0.669	-0.022
NOD	1.258	1.71
NZO	-0.525	0.363
PWK	0.674	0.482
H37Rv_KO_CtpC	0.221	0.437
H37Rv_KO_CtpD	0.608	0.656
H37Rv_KO_Rv1272	0.439	0.346
H37Rv_KO_SugABC	-0.122	0.607
H37Rv_KO_MbtN	0.611	0.892
Trans05	-0.161	0.842
macrophage_unactivated	-0.136	0.413
IL1	-1.317	-0.51
Rapamycin	-1.022	0.077
Tcell	0.202	-0.222
GMCSF	-1.172	-0.235
IFNab	-0.692	-0.187
IFNg	-0.484	0.094
IFNg_GMCSF1	-0.962	0.248
Rv1432_day32	-0.012	0.623
Rv1565c_day32	0.066	-0.316
secA2_input	-1.687	-0.726
delta_Rv3594	0.0	-0.494
delta_Rv3717	-0.029	-0.488
delta_Rv3811	0.034	-0.175
delta_Rv0954	-0.992	-0.552
PonA1	-0.226	-0.545
EccD1_KO	-0.414	-0.135
EspI_KO	0.328	0.225
PE35_KO	0.335	-0.152
PPE68_KO	0.442	-0.33
glycerol2	0.708	0.737
lignocerate	0.547	0.811
oleate	0.489	0.777
phosphatidylcholine	1.273	0.817
acetate	-0.033	0.243
glucAc	0.02	0.267
Rv0950ko	0.112	0.166
Rv1096ko	0.326	-0.621
Rv3684ko	0.0	-0.606
delta_otsA_trehalose	-0.654	-0.267