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 Rv2790c/ltp1

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

	Rv3452/cut4	Rv2790c/ltp1
Fe_supp_jason_reseq	0.373	-0.257
low_pH_jason_reseq	-1.705	0.738
NO_jason_reseq	-0.173	-0.234
B6_jason_reseq	-1.074	-1.072
MHCII_jason_reseq	-0.37	-1.234
Isoniazid02	0.857	3.176
Rifampicin4	1.17	-0.135
Ethambutol3	0.421	0.467
Meropenem3	1.543	-0.06
Vancomycin16	0.825	0.31
Rv2680_day32	0.819	0.581
H37Rv_KO_MarP	0.224	-0.137
hypoxia_3wks	0.044	0.853
hypoxia_6wks	0.382	0.896
glycerol	0.831	0.255
cholesterol	-0.722	-0.299
AJ	0.398	0.121
Bibs02	0.257	0.621
Bibs02c	-0.183	1.923
BL6	0.99	1.68
BL6a	0.476	1.97
BXD01	0.821	0.737
BXD010	0.553	1.57
BXD011	0.131	0.889
BXD03	0.407	0.743
BXD04	0.309	1.052
BXD05	1.164	0.719
BXD06	0.055	1.12
BXD07	0.359	1.075
BXD08	0.476	1.336
BXD09	0.485	1.277
CAST	0.452	-0.402
CCcont	0.77	0.419
DS01	0.914	1.372
DS02	0.427	0.61
DS04	0.618	0.198
DS0c	-0.398	0.374
GP01	1.36	1.39
GP02	-0.698	-0.145
GP0c	-0.184	1.166
NOD	-0.613	-1.045
NZO	0.321	-0.845
PWK	-0.024	0.247
H37Rv_KO_CtpC	0.913	2.096
H37Rv_KO_CtpD	-0.503	0.57
H37Rv_KO_Rv1272	-0.846	0.904
H37Rv_KO_SugABC	1.139	1.723
H37Rv_KO_MbtN	1.986	0.827
Trans05	0.815	1.644
macrophage_unactivated	1.228	0.338
IL1	-0.454	0.934
Rapamycin	-0.068	0.826
Tcell	0.0	0.671
GMCSF	0.042	0.945
IFNab	0.55	0.426
IFNg	0.409	0.465
IFNg_GMCSF1	1.197	0.443
Rv1432_day32	-0.351	-0.171
Rv1565c_day32	0.215	0.194
secA2_input	-0.543	-1.929
delta_Rv3594	0.012	0.493
delta_Rv3717	-0.059	0.366
delta_Rv3811	0.717	-0.177
delta_Rv0954	-0.165	-0.744
PonA1	1.252	-0.044
EccD1_KO	0.454	-0.375
EspI_KO	0.291	0.359
PE35_KO	-0.073	1.065
PPE68_KO	-0.214	0.944
glycerol2	0.817	1.265
lignocerate	0.877	0.608
oleate	1.375	1.745
phosphatidylcholine	1.111	1.486
acetate	0.218	-0.218
glucAc	0.259	-0.407
Rv0950ko	-0.181	-0.733
Rv1096ko	0.142	1.173
Rv3684ko	0.255	0.272
delta_otsA_trehalose	-1.347	-1.409