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 Rv0747/PE_PGRS10

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

	Rv0746/PE_PGRS9	Rv0747/PE_PGRS10
Fe_supp_jason_reseq	1.321	-0.48
low_pH_jason_reseq	1.84	0.709
NO_jason_reseq	-1.089	-0.247
B6_jason_reseq	1.7	0.173
MHCII_jason_reseq	2.165	0.941
Isoniazid02	-0.212	0.064
Rifampicin4	0.073	0.233
Ethambutol3	0.221	0.37
Meropenem3	-0.25	2.002
Vancomycin16	-0.91	-0.456
Rv2680_day32	-0.177	-0.171
H37Rv_KO_MarP	-0.289	0.027
hypoxia_3wks	0.104	0.243
hypoxia_6wks	0.186	0.127
glycerol	0.439	1.924
cholesterol	0.295	1.091
AJ	1.163	1.866
Bibs02	1.187	0.993
Bibs02c	0.964	1.223
BL6	-0.809	-1.133
BL6a	0.555	0.092
BXD01	1.277	-0.476
BXD010	-0.175	-0.958
BXD011	-0.519	-0.651
BXD03	0.536	-0.495
BXD04	1.072	0.014
BXD05	0.292	-0.687
BXD06	-0.544	-0.845
BXD07	-0.14	-0.629
BXD08	0.513	-0.556
BXD09	-0.046	-0.587
CAST	0.143	0.786
CCcont	-0.233	-0.733
DS01	-0.157	0.188
DS02	-0.145	0.569
DS04	1.39	0.134
DS0c	-0.107	0.335
GP01	0.683	-0.814
GP02	0.562	0.17
GP0c	1.072	-0.498
NOD	-0.35	0.415
NZO	1.115	0.503
PWK	0.426	0.863
H37Rv_KO_CtpC	0.552	-0.079
H37Rv_KO_CtpD	-0.27	-0.341
H37Rv_KO_Rv1272	0.543	-0.446
H37Rv_KO_SugABC	-1.076	0.338
H37Rv_KO_MbtN	-0.051	0.921
Trans05	0.231	-0.434
macrophage_unactivated	-0.41	-0.518
IL1	0.074	-0.561
Rapamycin	-0.399	-1.531
Tcell	0.951	-0.701
GMCSF	-0.135	0.694
IFNab	-0.916	-1.605
IFNg	-2.061	-1.334
IFNg_GMCSF1	0.654	0.069
Rv1432_day32	0.113	0.222
Rv1565c_day32	-0.766	-1.524
secA2_input	0.067	0.205
delta_Rv3594	0.174	-0.567
delta_Rv3717	0.294	-0.657
delta_Rv3811	-0.677	-0.564
delta_Rv0954	-0.416	-1.978
PonA1	-0.06	-0.891
EccD1_KO	1.72	0.763
EspI_KO	1.155	-0.117
PE35_KO	-0.245	0.088
PPE68_KO	0.666	0.096
glycerol2	0.144	0.464
lignocerate	0.242	0.615
oleate	0.315	0.469
phosphatidylcholine	0.553	0.564
acetate	0.213	0.785
glucAc	-0.085	0.8
Rv0950ko	-0.22	0.684
Rv1096ko	0.784	0.838
Rv3684ko	0.393	0.164
delta_otsA_trehalose	0.0	1.365