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 Rv3378c/-:

update plot	correlation	link to info on gene
Rv3429/PPE59	(cc=0.6567)	info on Rv3429/PPE59
Rv0403c/mmpS1	(cc=0.6371)	info on Rv0403c/mmpS1
Rv2107/PE22	(cc=0.6285)	info on Rv2107/PE22
Rv2929/-	(cc=0.6187)	info on Rv2929/-
Rv3383c/idsB	(cc=0.5997)	info on Rv3383c/idsB
Rv3555c/-	(cc=0.5967)	info on Rv3555c/-
Rv3146/nuoB	(cc=0.5797)	info on Rv3146/nuoB
Rv0822c/-	(cc=0.57)	info on Rv0822c/-
Rv0823c/-	(cc=0.5643)	info on Rv0823c/-
Rv1861/-	(cc=0.5616)	info on Rv1861/-

Correlation of Rv3378c/- with Rv1861/-

Normalized LFCs for Rv3378c/-:
(description and provenance of datasets)

	Rv3378c/-	Rv1861/-
Fe_supp_jason_reseq	0.09	-0.117
low_pH_jason_reseq	0.0	-1.655
NO_jason_reseq	0.562	0.428
B6_jason_reseq	-1.175	-1.122
MHCII_jason_reseq	-0.922	-0.956
Isoniazid02	0.188	-0.723
Rifampicin4	-0.384	-0.284
Ethambutol3	2.745	0.428
Meropenem3	-0.111	1.029
Vancomycin16	-0.122	-0.342
Rv2680_day32	0.219	0.683
H37Rv_KO_MarP	0.346	-0.428
hypoxia_3wks	0.55	0.63
hypoxia_6wks	0.288	1.165
glycerol	-0.791	-2.422
cholesterol	-0.435	-0.936
AJ	1.356	0.155
Bibs02	-0.123	0.057
Bibs02c	-0.141	-1.555
BL6	0.355	-0.072
BL6a	1.004	-0.35
BXD01	0.81	0.581
BXD010	2.138	0.628
BXD011	0.362	0.659
BXD03	1.461	0.255
BXD04	0.855	0.521
BXD05	0.736	-0.009
BXD06	1.411	0.903
BXD07	0.702	0.9
BXD08	1.308	0.989
BXD09	1.452	0.753
CAST	0.414	0.31
CCcont	0.497	-0.188
DS01	0.149	0.445
DS02	0.507	-0.199
DS04	1.699	0.604
DS0c	0.506	0.696
GP01	1.723	0.859
GP02	1.343	1.048
GP0c	0.76	0.809
NOD	0.0	0.861
NZO	0.465	0.334
PWK	0.995	0.527
H37Rv_KO_CtpC	1.423	1.449
H37Rv_KO_CtpD	1.728	1.112
H37Rv_KO_Rv1272	1.589	0.338
H37Rv_KO_SugABC	0.462	1.671
H37Rv_KO_MbtN	0.391	0.74
Trans05	1.529	0.734
macrophage_unactivated	0.17	0.12
IL1	0.16	-0.617
Rapamycin	-0.945	0.0
Tcell	0.176	-0.192
GMCSF	-0.636	-0.396
IFNab	-0.729	-0.453
IFNg	-0.644	-0.363
IFNg_GMCSF1	-1.191	-0.167
Rv1432_day32	0.0	0.386
Rv1565c_day32	-0.464	0.297
secA2_input	-0.174	-0.194
delta_Rv3594	-0.85	-0.11
delta_Rv3717	-0.7	-0.41
delta_Rv3811	0.0	-0.556
delta_Rv0954	0.074	0.417
PonA1	-0.547	-0.129
EccD1_KO	-0.171	-0.046
EspI_KO	0.55	0.22
PE35_KO	-0.475	-0.064
PPE68_KO	0.0	0.352
glycerol2	1.334	-0.149
lignocerate	-0.751	-0.505
oleate	0.044	0.411
phosphatidylcholine	0.209	-0.101
acetate	-0.522	-0.427
glucAc	-0.638	-1.002
Rv0950ko	1.701	1.061
Rv1096ko	1.007	-0.196
Rv3684ko	0.757	-1.055
delta_otsA_trehalose	0.435	0.247