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 Rv2590/fadD9

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

	Rv3452/cut4	Rv2590/fadD9
Fe_supp_jason_reseq	0.373	-0.251
low_pH_jason_reseq	-1.705	-1.092
NO_jason_reseq	-0.173	-0.344
B6_jason_reseq	-1.074	-0.253
MHCII_jason_reseq	-0.37	-0.336
Isoniazid02	0.857	0.586
Rifampicin4	1.17	0.217
Ethambutol3	0.421	0.643
Meropenem3	1.543	0.516
Vancomycin16	0.825	0.013
Rv2680_day32	0.819	0.1
H37Rv_KO_MarP	0.224	0.096
hypoxia_3wks	0.044	0.263
hypoxia_6wks	0.382	0.228
glycerol	0.831	0.034
cholesterol	-0.722	0.205
AJ	0.398	0.151
Bibs02	0.257	0.007
Bibs02c	-0.183	-0.168
BL6	0.99	-0.06
BL6a	0.476	-0.089
BXD01	0.821	0.076
BXD010	0.553	0.181
BXD011	0.131	0.198
BXD03	0.407	0.084
BXD04	0.309	-0.004
BXD05	1.164	-0.069
BXD06	0.055	0.048
BXD07	0.359	0.335
BXD08	0.476	-0.078
BXD09	0.485	0.211
CAST	0.452	-0.063
CCcont	0.77	-0.547
DS01	0.914	0.048
DS02	0.427	0.058
DS04	0.618	0.101
DS0c	-0.398	0.182
GP01	1.36	0.262
GP02	-0.698	0.212
GP0c	-0.184	-0.081
NOD	-0.613	-0.023
NZO	0.321	0.299
PWK	-0.024	0.065
H37Rv_KO_CtpC	0.913	-0.045
H37Rv_KO_CtpD	-0.503	0.414
H37Rv_KO_Rv1272	-0.846	0.28
H37Rv_KO_SugABC	1.139	0.571
H37Rv_KO_MbtN	1.986	0.293
Trans05	0.815	0.185
macrophage_unactivated	1.228	0.42
IL1	-0.454	0.653
Rapamycin	-0.068	0.663
Tcell	0.0	-0.075
GMCSF	0.042	0.462
IFNab	0.55	0.565
IFNg	0.409	0.265
IFNg_GMCSF1	1.197	0.145
Rv1432_day32	-0.351	0.389
Rv1565c_day32	0.215	-0.34
secA2_input	-0.543	0.063
delta_Rv3594	0.012	0.35
delta_Rv3717	-0.059	0.266
delta_Rv3811	0.717	-0.065
delta_Rv0954	-0.165	0.096
PonA1	1.252	0.328
EccD1_KO	0.454	0.263
EspI_KO	0.291	0.759
PE35_KO	-0.073	-0.096
PPE68_KO	-0.214	-0.019
glycerol2	0.817	0.639
lignocerate	0.877	0.566
oleate	1.375	0.929
phosphatidylcholine	1.111	0.831
acetate	0.218	-0.165
glucAc	0.259	-0.27
Rv0950ko	-0.181	0.329
Rv1096ko	0.142	0.428
Rv3684ko	0.255	0.396
delta_otsA_trehalose	-1.347	-0.627