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 Rv3452/cut4:

update plot	correlation	link to info on gene
Rv3470c/ilvB2	(cc=0.4339)	info on Rv3470c/ilvB2
Rv0476/-	(cc=0.4072)	info on Rv0476/-
Rv0492c/-	(cc=0.3998)	info on Rv0492c/-
Rv2790c/ltp1	(cc=0.3959)	info on Rv2790c/ltp1
Rv2590/fadD9	(cc=0.3957)	info on Rv2590/fadD9
Rv1523/-	(cc=0.3898)	info on Rv1523/-
Rv0762c/-	(cc=0.3832)	info on Rv0762c/-
Rv2836c/dinF	(cc=0.3812)	info on Rv2836c/dinF
Rv3835/-	(cc=0.381)	info on Rv3835/-
Rv1489/-	(cc=0.3804)	info on Rv1489/-

Correlation of Rv3452/cut4 with Rv0476/-

Normalized LFCs for Rv3452/cut4:
(description and provenance of datasets)

	Rv3452/cut4	Rv0476/-
Fe_supp_jason_reseq	0.373	-0.401
low_pH_jason_reseq	-1.705	-0.773
NO_jason_reseq	-0.173	0.092
B6_jason_reseq	-1.074	-1.211
MHCII_jason_reseq	-0.37	0.065
Isoniazid02	0.857	0.955
Rifampicin4	1.17	0.736
Ethambutol3	0.421	1.192
Meropenem3	1.543	1.353
Vancomycin16	0.825	0.722
Rv2680_day32	0.819	1.297
H37Rv_KO_MarP	0.224	-1.099
hypoxia_3wks	0.044	1.105
hypoxia_6wks	0.382	1.117
glycerol	0.831	-2.055
cholesterol	-0.722	-1.374
AJ	0.398	-0.376
Bibs02	0.257	-0.411
Bibs02c	-0.183	-1.184
BL6	0.99	-0.434
BL6a	0.476	-0.535
BXD01	0.821	0.481
BXD010	0.553	0.742
BXD011	0.131	0.567
BXD03	0.407	0.28
BXD04	0.309	0.913
BXD05	1.164	0.417
BXD06	0.055	0.391
BXD07	0.359	0.877
BXD08	0.476	0.675
BXD09	0.485	0.248
CAST	0.452	-1.175
CCcont	0.77	0.057
DS01	0.914	0.05
DS02	0.427	-0.213
DS04	0.618	0.624
DS0c	-0.398	-0.561
GP01	1.36	0.17
GP02	-0.698	0.266
GP0c	-0.184	0.633
NOD	-0.613	0.392
NZO	0.321	0.5
PWK	-0.024	-0.036
H37Rv_KO_CtpC	0.913	-0.065
H37Rv_KO_CtpD	-0.503	0.833
H37Rv_KO_Rv1272	-0.846	0.087
H37Rv_KO_SugABC	1.139	0.658
H37Rv_KO_MbtN	1.986	1.183
Trans05	0.815	0.228
macrophage_unactivated	1.228	0.312
IL1	-0.454	-0.967
Rapamycin	-0.068	-0.184
Tcell	0.0	-0.244
GMCSF	0.042	0.211
IFNab	0.55	0.84
IFNg	0.409	0.708
IFNg_GMCSF1	1.197	0.06
Rv1432_day32	-0.351	1.622
Rv1565c_day32	0.215	-0.295
secA2_input	-0.543	-1.035
delta_Rv3594	0.012	-0.318
delta_Rv3717	-0.059	0.38
delta_Rv3811	0.717	0.489
delta_Rv0954	-0.165	-0.881
PonA1	1.252	-0.275
EccD1_KO	0.454	-1.496
EspI_KO	0.291	-0.299
PE35_KO	-0.073	-1.423
PPE68_KO	-0.214	-0.995
glycerol2	0.817	2.023
lignocerate	0.877	0.267
oleate	1.375	2.439
phosphatidylcholine	1.111	0.097
acetate	0.218	-0.04
glucAc	0.259	-0.154
Rv0950ko	-0.181	-0.413
Rv1096ko	0.142	-0.929
Rv3684ko	0.255	-0.38
delta_otsA_trehalose	-1.347	-0.738