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 Rv3512/PE_PGRS56:

update plot	correlation	link to info on gene
Rv1087/PE_PGRS21	(cc=0.7395)	info on Rv1087/PE_PGRS21
Rv3508/PE_PGRS54	(cc=0.7258)	info on Rv3508/PE_PGRS54
Rv3514/PE_PGRS57	(cc=0.7087)	info on Rv3514/PE_PGRS57
Rv1091/PE_PGRS22	(cc=0.6852)	info on Rv1091/PE_PGRS22
Rv3345c/PE_PGRS50	(cc=0.6749)	info on Rv3345c/PE_PGRS50
Rv0833/PE_PGRS13	(cc=0.6545)	info on Rv0833/PE_PGRS13
Rv2815c/-	(cc=0.5911)	info on Rv2815c/-
Rv3511/PE_PGRS55	(cc=0.5701)	info on Rv3511/PE_PGRS55
Rv2479c/-	(cc=0.5599)	info on Rv2479c/-
Rv2814c/-	(cc=0.5554)	info on Rv2814c/-

Correlation of Rv3512/PE_PGRS56 with Rv2815c/-

Normalized LFCs for Rv3512/PE_PGRS56:
(description and provenance of datasets)

	Rv3512/PE_PGRS56	Rv2815c/-
Fe_supp_jason_reseq	-0.587	-0.516
low_pH_jason_reseq	-1.091	0.323
NO_jason_reseq	-0.176	0.0
B6_jason_reseq	-0.322	-0.468
MHCII_jason_reseq	0.123	-0.549
Isoniazid02	-1.909	-0.419
Rifampicin4	-0.647	0.42
Ethambutol3	-0.537	1.342
Meropenem3	-0.737	-0.404
Vancomycin16	-0.963	-0.268
Rv2680_day32	0.529	-0.306
H37Rv_KO_MarP	0.0	-0.224
hypoxia_3wks	-0.183	1.033
hypoxia_6wks	-1.13	-0.061
glycerol	1.981	0.184
cholesterol	1.209	0.518
AJ	2.276	1.906
Bibs02	1.27	0.49
Bibs02c	1.576	1.058
BL6	0.263	0.298
BL6a	0.914	1.032
BXD01	0.695	0.771
BXD010	1.102	0.936
BXD011	0.49	0.669
BXD03	0.573	1.014
BXD04	0.859	0.503
BXD05	0.764	1.106
BXD06	0.075	0.632
BXD07	0.291	0.804
BXD08	0.341	0.535
BXD09	0.36	0.619
CAST	0.484	0.896
CCcont	0.24	0.213
DS01	0.38	0.691
DS02	0.922	0.846
DS04	0.11	1.01
DS0c	-0.129	1.001
GP01	0.561	1.181
GP02	0.553	1.438
GP0c	0.738	0.662
NOD	0.0	1.009
NZO	1.326	1.526
PWK	0.674	2.023
H37Rv_KO_CtpC	0.261	0.926
H37Rv_KO_CtpD	0.584	0.674
H37Rv_KO_Rv1272	1.177	0.336
H37Rv_KO_SugABC	0.381	0.802
H37Rv_KO_MbtN	-0.271	1.413
Trans05	1.157	0.686
macrophage_unactivated	-0.537	0.0
IL1	-1.978	-0.205
Rapamycin	-1.795	-0.69
Tcell	-1.652	-1.359
GMCSF	-0.779	-1.172
IFNab	-2.283	-1.342
IFNg	-1.157	-0.641
IFNg_GMCSF1	-0.349	-0.443
Rv1432_day32	0.252	1.542
Rv1565c_day32	-1.275	-0.294
secA2_input	0.0	0.756
delta_Rv3594	0.272	0.142
delta_Rv3717	-0.629	-0.403
delta_Rv3811	-0.253	-0.451
delta_Rv0954	-2.288	-0.186
PonA1	0.714	-0.524
EccD1_KO	0.418	-0.276
EspI_KO	-0.451	1.035
PE35_KO	-0.916	0.341
PPE68_KO	-0.685	0.086
glycerol2	0.109	-0.318
lignocerate	0.505	-0.559
oleate	-0.515	-0.573
phosphatidylcholine	0.0	-0.147
acetate	1.225	1.305
glucAc	1.367	1.68
Rv0950ko	-0.63	0.552
Rv1096ko	0.115	0.139
Rv3684ko	-0.065	-0.111
delta_otsA_trehalose	0.366	-0.906