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 Rv2542/-:

update plot	correlation	link to info on gene
Rv2915c/-	(cc=0.4718)	info on Rv2915c/-
Rv0517/-	(cc=0.4411)	info on Rv0517/-
Rv2226/-	(cc=0.4188)	info on Rv2226/-
Rv3129/-	(cc=0.4055)	info on Rv3129/-
Rv2322c/rocD1	(cc=0.4048)	info on Rv2322c/rocD1
Rv2306B/-	(cc=0.402)	info on Rv2306B/-
Rv0406c/-	(cc=0.4001)	info on Rv0406c/-
Rv1250/-	(cc=0.3984)	info on Rv1250/-
Rv0895/-	(cc=0.3963)	info on Rv0895/-
Rv0265c/-	(cc=0.3953)	info on Rv0265c/-

Correlation of Rv2542/- with Rv0517/-

Normalized LFCs for Rv2542/-:
(description and provenance of datasets)

	Rv2542/-	Rv0517/-
Fe_supp_jason_reseq	0.513	-0.564
low_pH_jason_reseq	-0.82	-1.084
NO_jason_reseq	-0.257	-0.263
B6_jason_reseq	-0.109	-0.347
MHCII_jason_reseq	0.142	0.223
Isoniazid02	-0.195	-0.749
Rifampicin4	0.273	-0.577
Ethambutol3	-0.235	-1.876
Meropenem3	0.283	-0.561
Vancomycin16	-0.093	-0.623
Rv2680_day32	0.538	0.452
H37Rv_KO_MarP	0.082	0.279
hypoxia_3wks	1.049	0.494
hypoxia_6wks	0.973	0.576
glycerol	-0.253	-0.511
cholesterol	-0.129	0.212
AJ	-0.146	-0.054
Bibs02	0.166	0.021
Bibs02c	0.74	0.277
BL6	-0.006	0.119
BL6a	0.415	-0.014
BXD01	-0.333	-0.317
BXD010	-0.075	-0.25
BXD011	-0.126	-0.329
BXD03	-0.761	0.154
BXD04	-0.518	-0.43
BXD05	-0.499	-0.165
BXD06	-0.007	-0.443
BXD07	-0.768	-0.403
BXD08	-0.365	-0.429
BXD09	-0.089	-0.213
CAST	-0.145	-0.692
CCcont	-0.303	-0.554
DS01	-0.115	0.209
DS02	0.805	0.044
DS04	1.072	0.101
DS0c	0.041	-0.016
GP01	-1.345	-0.922
GP02	-0.852	-1.025
GP0c	-0.191	-0.69
NOD	-0.153	-0.275
NZO	-0.967	-0.34
PWK	0.161	-0.827
H37Rv_KO_CtpC	0.229	-0.345
H37Rv_KO_CtpD	-0.567	-0.219
H37Rv_KO_Rv1272	-0.59	0.38
H37Rv_KO_SugABC	0.65	0.478
H37Rv_KO_MbtN	-0.476	-0.66
Trans05	-0.663	-0.645
macrophage_unactivated	-0.439	0.161
IL1	0.193	0.131
Rapamycin	0.47	0.694
Tcell	0.166	-0.049
GMCSF	-0.119	0.04
IFNab	0.0	0.565
IFNg	0.174	0.099
IFNg_GMCSF1	0.0	0.069
Rv1432_day32	0.648	0.984
Rv1565c_day32	-0.093	-0.553
secA2_input	0.775	0.283
delta_Rv3594	-0.786	0.106
delta_Rv3717	-0.122	-0.145
delta_Rv3811	-0.348	-0.178
delta_Rv0954	-0.053	0.128
PonA1	-0.518	0.225
EccD1_KO	0.589	0.539
EspI_KO	0.511	-0.128
PE35_KO	0.405	-0.105
PPE68_KO	0.614	-0.355
glycerol2	-0.021	0.163
lignocerate	-0.074	0.364
oleate	-0.176	-0.018
phosphatidylcholine	-0.053	0.543
acetate	-0.554	-0.389
glucAc	-0.136	0.112
Rv0950ko	0.944	-0.41
Rv1096ko	-0.021	-0.537
Rv3684ko	0.164	-0.082
delta_otsA_trehalose	-0.109	-0.331