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 Rv1091/PE_PGRS22

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

	Rv3512/PE_PGRS56	Rv1091/PE_PGRS22
Fe_supp_jason_reseq	-0.587	-0.612
low_pH_jason_reseq	-1.091	-0.318
NO_jason_reseq	-0.176	-0.087
B6_jason_reseq	-0.322	-0.686
MHCII_jason_reseq	0.123	0.273
Isoniazid02	-1.909	-1.317
Rifampicin4	-0.647	0.563
Ethambutol3	-0.537	0.074
Meropenem3	-0.737	0.268
Vancomycin16	-0.963	-0.348
Rv2680_day32	0.529	-0.091
H37Rv_KO_MarP	0.0	-0.202
hypoxia_3wks	-0.183	0.171
hypoxia_6wks	-1.13	0.177
glycerol	1.981	1.072
cholesterol	1.209	0.81
AJ	2.276	0.919
Bibs02	1.27	1.439
Bibs02c	1.576	0.985
BL6	0.263	-1.01
BL6a	0.914	0.531
BXD01	0.695	0.349
BXD010	1.102	0.155
BXD011	0.49	0.277
BXD03	0.573	0.043
BXD04	0.859	0.058
BXD05	0.764	0.473
BXD06	0.075	-0.258
BXD07	0.291	0.422
BXD08	0.341	0.103
BXD09	0.36	-0.046
CAST	0.484	0.247
CCcont	0.24	-0.609
DS01	0.38	0.45
DS02	0.922	0.688
DS04	0.11	0.568
DS0c	-0.129	0.035
GP01	0.561	0.505
GP02	0.553	0.547
GP0c	0.738	0.472
NOD	0.0	0.488
NZO	1.326	-0.133
PWK	0.674	0.666
H37Rv_KO_CtpC	0.261	0.076
H37Rv_KO_CtpD	0.584	0.865
H37Rv_KO_Rv1272	1.177	2.015
H37Rv_KO_SugABC	0.381	-0.529
H37Rv_KO_MbtN	-0.271	-0.667
Trans05	1.157	0.35
macrophage_unactivated	-0.537	-0.527
IL1	-1.978	-1.883
Rapamycin	-1.795	-1.676
Tcell	-1.652	-1.245
GMCSF	-0.779	-0.747
IFNab	-2.283	-2.515
IFNg	-1.157	-1.307
IFNg_GMCSF1	-0.349	-0.669
Rv1432_day32	0.252	0.441
Rv1565c_day32	-1.275	-0.924
secA2_input	0.0	-0.211
delta_Rv3594	0.272	0.229
delta_Rv3717	-0.629	0.294
delta_Rv3811	-0.253	-0.168
delta_Rv0954	-2.288	-1.098
PonA1	0.714	0.21
EccD1_KO	0.418	0.513
EspI_KO	-0.451	-0.459
PE35_KO	-0.916	0.067
PPE68_KO	-0.685	0.074
glycerol2	0.109	-0.666
lignocerate	0.505	-1.094
oleate	-0.515	-0.102
phosphatidylcholine	0.0	-0.564
acetate	1.225	-0.557
glucAc	1.367	-0.543
Rv0950ko	-0.63	0.476
Rv1096ko	0.115	1.215
Rv3684ko	-0.065	0.19
delta_otsA_trehalose	0.366	0.272