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 Rv0112/gca:

update plot	correlation	link to info on gene
Rv2430c/PPE41	(cc=0.6914)	info on Rv2430c/PPE41
Rv1918c/PPE35	(cc=0.6414)	info on Rv1918c/PPE35
Rv2735c/-	(cc=0.6295)	info on Rv2735c/-
Rv0907/-	(cc=0.6282)	info on Rv0907/-
Rv0469/umaA	(cc=0.6168)	info on Rv0469/umaA
Rv3218/-	(cc=0.6008)	info on Rv3218/-
Rv0059/-	(cc=0.5935)	info on Rv0059/-
Rv1505c/-	(cc=0.5928)	info on Rv1505c/-
Rv1059/-	(cc=0.5885)	info on Rv1059/-
Rv3864/espE	(cc=0.587)	info on Rv3864/espE

Correlation of Rv0112/gca with Rv0907/-

Normalized LFCs for Rv0112/gca:
(description and provenance of datasets)

	Rv0112/gca	Rv0907/-
Fe_supp_jason_reseq	0.415	-0.147
low_pH_jason_reseq	1.335	0.284
NO_jason_reseq	0.171	-0.507
B6_jason_reseq	0.292	-0.417
MHCII_jason_reseq	-0.342	0.963
Isoniazid02	0.636	1.505
Rifampicin4	-0.165	-0.601
Ethambutol3	1.454	1.574
Meropenem3	-0.359	0.302
Vancomycin16	0.157	0.0
Rv2680_day32	-0.383	0.476
H37Rv_KO_MarP	-0.223	-0.042
hypoxia_3wks	0.53	0.096
hypoxia_6wks	0.142	0.472
glycerol	-0.753	-0.05
cholesterol	-0.469	0.167
AJ	1.239	0.413
Bibs02	-0.682	-0.339
Bibs02c	0.887	0.835
BL6	0.839	0.248
BL6a	1.663	0.824
BXD01	1.652	0.583
BXD010	1.81	0.912
BXD011	2.088	1.083
BXD03	1.673	1.105
BXD04	0.581	0.365
BXD05	0.747	0.371
BXD06	1.26	0.533
BXD07	1.073	1.306
BXD08	0.987	0.881
BXD09	1.384	0.44
CAST	0.569	0.055
CCcont	0.701	1.408
DS01	0.236	0.421
DS02	0.711	0.476
DS04	0.254	0.572
DS0c	0.815	0.052
GP01	0.067	0.921
GP02	0.109	0.165
GP0c	1.478	0.407
NOD	1.054	1.076
NZO	0.548	0.588
PWK	1.088	0.429
H37Rv_KO_CtpC	0.966	0.753
H37Rv_KO_CtpD	1.023	0.506
H37Rv_KO_Rv1272	1.427	1.76
H37Rv_KO_SugABC	0.976	1.423
H37Rv_KO_MbtN	1.612	0.709
Trans05	2.074	0.385
macrophage_unactivated	0.139	-0.499
IL1	0.0	-0.151
Rapamycin	0.203	0.436
Tcell	0.554	0.463
GMCSF	0.655	0.375
IFNab	-0.429	0.496
IFNg	0.345	0.257
IFNg_GMCSF1	0.779	0.446
Rv1432_day32	-0.164	-0.094
Rv1565c_day32	0.065	-0.539
secA2_input	-1.342	-0.188
delta_Rv3594	0.035	0.0
delta_Rv3717	0.141	-0.771
delta_Rv3811	-0.219	0.0
delta_Rv0954	-0.726	-0.686
PonA1	0.382	-0.032
EccD1_KO	-0.572	0.0
EspI_KO	-1.132	0.0
PE35_KO	-0.755	-0.473
PPE68_KO	-0.691	-0.63
glycerol2	-0.234	-0.241
lignocerate	-0.374	-0.019
oleate	0.474	-0.55
phosphatidylcholine	-0.056	-0.092
acetate	-0.17	0.0
glucAc	-0.722	-0.178
Rv0950ko	0.374	0.0
Rv1096ko	-0.48	0.522
Rv3684ko	-0.599	0.196
delta_otsA_trehalose	2.09	2.255