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 Rv3766/-

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

	Rv0746/PE_PGRS9	Rv3766/-
Fe_supp_jason_reseq	1.321	1.023
low_pH_jason_reseq	1.84	-0.11
NO_jason_reseq	-1.089	-0.042
B6_jason_reseq	1.7	0.625
MHCII_jason_reseq	2.165	2.035
Isoniazid02	-0.212	0.402
Rifampicin4	0.073	0.412
Ethambutol3	0.221	0.185
Meropenem3	-0.25	0.056
Vancomycin16	-0.91	-0.085
Rv2680_day32	-0.177	1.218
H37Rv_KO_MarP	-0.289	0.343
hypoxia_3wks	0.104	-0.319
hypoxia_6wks	0.186	-0.345
glycerol	0.439	-0.192
cholesterol	0.295	0.302
AJ	1.163	1.839
Bibs02	1.187	0.527
Bibs02c	0.964	-0.317
BL6	-0.809	-1.424
BL6a	0.555	0.716
BXD01	1.277	0.644
BXD010	-0.175	0.634
BXD011	-0.519	-0.149
BXD03	0.536	0.178
BXD04	1.072	1.352
BXD05	0.292	0.605
BXD06	-0.544	0.933
BXD07	-0.14	0.301
BXD08	0.513	0.3
BXD09	-0.046	1.073
CAST	0.143	1.126
CCcont	-0.233	-1.082
DS01	-0.157	0.57
DS02	-0.145	0.0
DS04	1.39	0.603
DS0c	-0.107	0.416
GP01	0.683	-0.485
GP02	0.562	-0.672
GP0c	1.072	-0.891
NOD	-0.35	2.341
NZO	1.115	1.821
PWK	0.426	1.113
H37Rv_KO_CtpC	0.552	0.884
H37Rv_KO_CtpD	-0.27	1.459
H37Rv_KO_Rv1272	0.543	0.578
H37Rv_KO_SugABC	-1.076	0.358
H37Rv_KO_MbtN	-0.051	-0.789
Trans05	0.231	-0.259
macrophage_unactivated	-0.41	-0.988
IL1	0.074	-0.771
Rapamycin	-0.399	-1.571
Tcell	0.951	-0.482
GMCSF	-0.135	-0.549
IFNab	-0.916	-1.587
IFNg	-2.061	-1.269
IFNg_GMCSF1	0.654	-0.496
Rv1432_day32	0.113	-0.257
Rv1565c_day32	-0.766	2.072
secA2_input	0.067	0.067
delta_Rv3594	0.174	0.439
delta_Rv3717	0.294	0.409
delta_Rv3811	-0.677	0.115
delta_Rv0954	-0.416	0.992
PonA1	-0.06	-0.485
EccD1_KO	1.72	1.605
EspI_KO	1.155	2.878
PE35_KO	-0.245	-2.526
PPE68_KO	0.666	1.945
glycerol2	0.144	1.666
lignocerate	0.242	1.218
oleate	0.315	0.768
phosphatidylcholine	0.553	1.34
acetate	0.213	-0.69
glucAc	-0.085	0.467
Rv0950ko	-0.22	0.066
Rv1096ko	0.784	0.317
Rv3684ko	0.393	0.878
delta_otsA_trehalose	0.0	0.05