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 Rv2946c/pks1:

update plot	correlation	link to info on gene
Rv2942/mmpL7	(cc=0.6788)	info on Rv2942/mmpL7
Rv2945c/lppX	(cc=0.6517)	info on Rv2945c/lppX
Rv2936/drrA	(cc=0.5864)	info on Rv2936/drrA
Rv1109c/-	(cc=0.5669)	info on Rv1109c/-
Rv3200c/-	(cc=0.5456)	info on Rv3200c/-
Rv2937/drrB	(cc=0.5327)	info on Rv2937/drrB
Rv2938/drrC	(cc=0.5147)	info on Rv2938/drrC
Rv2218/lipA	(cc=0.5122)	info on Rv2218/lipA
Rv2498c/citE	(cc=0.5091)	info on Rv2498c/citE
Rv1829/-	(cc=0.5077)	info on Rv1829/-

Correlation of Rv2946c/pks1 with Rv2218/lipA

Normalized LFCs for Rv2946c/pks1:
(description and provenance of datasets)

	Rv2946c/pks1	Rv2218/lipA
Fe_supp_jason_reseq	0.14	1.228
low_pH_jason_reseq	-0.903	-0.371
NO_jason_reseq	-0.987	-0.914
B6_jason_reseq	-0.23	0.991
MHCII_jason_reseq	-0.172	0.572
Isoniazid02	-0.068	0.0
Rifampicin4	-0.171	0.0
Ethambutol3	0.705	0.845
Meropenem3	0.303	0.435
Vancomycin16	-0.082	0.0
Rv2680_day32	-1.387	0.0
H37Rv_KO_MarP	-0.703	0.0
hypoxia_3wks	1.168	0.933
hypoxia_6wks	1.247	0.334
glycerol	0.455	1.24
cholesterol	0.541	0.435
AJ	-0.968	-0.346
Bibs02	0.162	0.0
Bibs02c	0.135	0.274
BL6	-0.149	1.346
BL6a	0.039	0.595
BXD01	0.222	0.392
BXD010	-0.079	0.787
BXD011	0.074	0.167
BXD03	0.253	-0.202
BXD04	0.486	0.979
BXD05	-0.083	1.38
BXD06	0.009	0.82
BXD07	0.036	1.345
BXD08	0.473	1.255
BXD09	-0.047	0.916
CAST	-1.078	0.0
CCcont	0.329	0.667
DS01	0.015	0.159
DS02	-0.358	-0.704
DS04	0.298	1.036
DS0c	-0.291	0.146
GP01	0.518	0.067
GP02	-0.051	2.166
GP0c	0.399	0.0
NOD	-1.245	-0.727
NZO	-1.039	-0.845
PWK	-0.838	-0.635
H37Rv_KO_CtpC	-0.181	-0.688
H37Rv_KO_CtpD	0.05	1.454
H37Rv_KO_Rv1272	-0.418	-0.21
H37Rv_KO_SugABC	0.841	2.612
H37Rv_KO_MbtN	0.494	-0.24
Trans05	-0.155	-0.195
macrophage_unactivated	0.259	0.83
IL1	0.43	0.78
Rapamycin	0.528	1.046
Tcell	0.694	1.352
GMCSF	0.177	1.281
IFNab	0.877	1.865
IFNg	-0.061	1.97
IFNg_GMCSF1	-0.025	1.304
Rv1432_day32	-0.947	0.0
Rv1565c_day32	-0.253	-0.235
secA2_input	-0.39	0.092
delta_Rv3594	0.639	1.53
delta_Rv3717	0.094	0.228
delta_Rv3811	0.634	0.507
delta_Rv0954	0.592	-0.266
PonA1	0.248	-0.372
EccD1_KO	-0.214	0.0
EspI_KO	0.325	1.417
PE35_KO	-0.053	0.467
PPE68_KO	-0.029	0.262
glycerol2	0.0	-0.27
lignocerate	-0.195	-1.078
oleate	0.121	0.523
phosphatidylcholine	0.041	0.161
acetate	-0.564	0.369
glucAc	-0.461	-1.164
Rv0950ko	0.181	0.639
Rv1096ko	0.027	1.016
Rv3684ko	-0.354	-0.524
delta_otsA_trehalose	-0.527	1.098