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 Rv0746/PE_PGRS9:

update plot	correlation	link to info on gene
Rv0332/-	(cc=0.4071)	info on Rv0332/-
Rv1060/-	(cc=0.4057)	info on Rv1060/-
Rv1691/-	(cc=0.3945)	info on Rv1691/-
Rv0747/PE_PGRS10	(cc=0.387)	info on Rv0747/PE_PGRS10
Rv1647/-	(cc=0.3855)	info on Rv1647/-
Rv3508/PE_PGRS54	(cc=0.3846)	info on Rv3508/PE_PGRS54
Rv1180/pks3	(cc=0.3818)	info on Rv1180/pks3
Rv2645/-	(cc=0.3685)	info on Rv2645/-
Rv0428c/-	(cc=0.3647)	info on Rv0428c/-
Rv3766/-	(cc=0.3644)	info on Rv3766/-

Correlation of Rv0746/PE_PGRS9 with Rv1691/-

Normalized LFCs for Rv0746/PE_PGRS9:
(description and provenance of datasets)

	Rv0746/PE_PGRS9	Rv1691/-
Fe_supp_jason_reseq	1.321	2.021
low_pH_jason_reseq	1.84	1.494
NO_jason_reseq	-1.089	2.197
B6_jason_reseq	1.7	3.131
MHCII_jason_reseq	2.165	1.251
Isoniazid02	-0.212	-0.965
Rifampicin4	0.073	1.072
Ethambutol3	0.221	1.626
Meropenem3	-0.25	-0.655
Vancomycin16	-0.91	1.051
Rv2680_day32	-0.177	0.168
H37Rv_KO_MarP	-0.289	0.789
hypoxia_3wks	0.104	-2.006
hypoxia_6wks	0.186	-1.311
glycerol	0.439	2.146
cholesterol	0.295	0.7
AJ	1.163	-0.304
Bibs02	1.187	-0.666
Bibs02c	0.964	0.124
BL6	-0.809	-0.254
BL6a	0.555	0.438
BXD01	1.277	1.095
BXD010	-0.175	0.928
BXD011	-0.519	-0.167
BXD03	0.536	0.299
BXD04	1.072	3.773
BXD05	0.292	0.485
BXD06	-0.544	0.593
BXD07	-0.14	0.558
BXD08	0.513	2.006
BXD09	-0.046	0.238
CAST	0.143	1.935
CCcont	-0.233	0.538
DS01	-0.157	-0.149
DS02	-0.145	0.129
DS04	1.39	-0.394
DS0c	-0.107	-0.79
GP01	0.683	0.266
GP02	0.562	1.336
GP0c	1.072	1.093
NOD	-0.35	-0.818
NZO	1.115	0.538
PWK	0.426	0.871
H37Rv_KO_CtpC	0.552	1.365
H37Rv_KO_CtpD	-0.27	-0.08
H37Rv_KO_Rv1272	0.543	0.163
H37Rv_KO_SugABC	-1.076	-0.278
H37Rv_KO_MbtN	-0.051	0.921
Trans05	0.231	-0.171
macrophage_unactivated	-0.41	-0.275
IL1	0.074	-1.148
Rapamycin	-0.399	-0.267
Tcell	0.951	1.619
GMCSF	-0.135	-1.328
IFNab	-0.916	-0.547
IFNg	-2.061	-1.034
IFNg_GMCSF1	0.654	-1.216
Rv1432_day32	0.113	0.155
Rv1565c_day32	-0.766	-0.182
secA2_input	0.067	1.052
delta_Rv3594	0.174	-0.291
delta_Rv3717	0.294	1.679
delta_Rv3811	-0.677	0.654
delta_Rv0954	-0.416	-2.95
PonA1	-0.06	-0.143
EccD1_KO	1.72	1.312
EspI_KO	1.155	0.841
PE35_KO	-0.245	1.444
PPE68_KO	0.666	0.771
glycerol2	0.144	0.202
lignocerate	0.242	0.175
oleate	0.315	-0.352
phosphatidylcholine	0.553	0.104
acetate	0.213	0.56
glucAc	-0.085	0.0
Rv0950ko	-0.22	-0.335
Rv1096ko	0.784	3.251
Rv3684ko	0.393	1.615
delta_otsA_trehalose	0.0	-1.218