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 Rv1749c/-:

update plot	correlation	link to info on gene
Rv1526c/-	(cc=0.5462)	info on Rv1526c/-
Rv3213c/-	(cc=0.5165)	info on Rv3213c/-
Rv3429/PPE59	(cc=0.5102)	info on Rv3429/PPE59
Rv1583c/-	(cc=0.5057)	info on Rv1583c/-
Rv0028/-	(cc=0.5054)	info on Rv0028/-
Rv0042c/-	(cc=0.4944)	info on Rv0042c/-
Rv3217c/-	(cc=0.4881)	info on Rv3217c/-
Rv2237/-	(cc=0.4811)	info on Rv2237/-
Rv1981c/nrdF1	(cc=0.4701)	info on Rv1981c/nrdF1
Rv0432/sodC	(cc=0.47)	info on Rv0432/sodC

Correlation of Rv1749c/- with Rv0028/-

Normalized LFCs for Rv1749c/-:
(description and provenance of datasets)

	Rv1749c/-	Rv0028/-
Fe_supp_jason_reseq	0.218	-0.319
low_pH_jason_reseq	0.11	-1.246
NO_jason_reseq	0.278	0.273
B6_jason_reseq	-0.818	-0.253
MHCII_jason_reseq	-0.357	-0.418
Isoniazid02	-0.445	0.102
Rifampicin4	-0.542	-0.349
Ethambutol3	-0.158	-0.185
Meropenem3	0.097	-0.037
Vancomycin16	-0.366	0.082
Rv2680_day32	-1.062	0.862
H37Rv_KO_MarP	-0.278	0.158
hypoxia_3wks	-0.666	-0.383
hypoxia_6wks	-0.714	-0.136
glycerol	-1.006	-1.871
cholesterol	-0.46	-1.108
AJ	-0.05	-1.257
Bibs02	-0.378	-0.184
Bibs02c	-0.139	0.099
BL6	1.067	1.642
BL6a	0.242	1.119
BXD01	0.192	1.186
BXD010	0.787	1.693
BXD011	0.486	0.977
BXD03	-0.291	1.352
BXD04	-0.064	1.079
BXD05	0.642	1.093
BXD06	0.111	1.113
BXD07	0.57	1.346
BXD08	0.547	1.232
BXD09	0.268	1.227
CAST	-0.118	0.325
CCcont	0.844	1.792
DS01	0.149	0.128
DS02	0.334	0.785
DS04	0.537	-1.078
DS0c	0.223	0.017
GP01	1.649	1.26
GP02	0.6	1.64
GP0c	1.255	-0.064
NOD	0.094	0.958
NZO	-0.276	0.53
PWK	-0.207	-0.396
H37Rv_KO_CtpC	-0.791	-0.221
H37Rv_KO_CtpD	0.967	1.855
H37Rv_KO_Rv1272	-0.149	0.476
H37Rv_KO_SugABC	1.05	1.616
H37Rv_KO_MbtN	-0.061	-0.531
Trans05	0.913	0.307
macrophage_unactivated	-0.196	0.013
IL1	-0.43	1.154
Rapamycin	-0.301	0.608
Tcell	-0.029	-0.306
GMCSF	0.327	0.726
IFNab	0.178	0.457
IFNg	0.024	0.011
IFNg_GMCSF1	0.795	0.924
Rv1432_day32	0.314	1.644
Rv1565c_day32	-2.443	-0.94
secA2_input	0.36	0.416
delta_Rv3594	0.45	0.018
delta_Rv3717	-0.011	-0.244
delta_Rv3811	0.109	-1.258
delta_Rv0954	0.205	0.039
PonA1	0.749	0.007
EccD1_KO	-0.118	0.069
EspI_KO	-0.06	-0.553
PE35_KO	-0.528	-0.082
PPE68_KO	-0.378	-0.045
glycerol2	0.668	0.406
lignocerate	1.269	0.897
oleate	-0.123	-0.418
phosphatidylcholine	0.859	0.318
acetate	1.322	0.73
glucAc	1.325	0.533
Rv0950ko	0.289	0.567
Rv1096ko	-0.642	0.437
Rv3684ko	-1.002	0.18
delta_otsA_trehalose	0.706	1.104