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 Rv1196/PPE18:

update plot	correlation	link to info on gene
Rv1194c/-	(cc=0.6576)	info on Rv1194c/-
Rv1195/PE13	(cc=0.6444)	info on Rv1195/PE13
Rv1872c/lldD2	(cc=0.5814)	info on Rv1872c/lldD2
Rv3223c/sigH	(cc=0.5787)	info on Rv3223c/sigH
Rv1364c/-	(cc=0.5578)	info on Rv1364c/-
Rv3152/nuoH	(cc=0.5339)	info on Rv3152/nuoH
Rv2107/PE22	(cc=0.5322)	info on Rv2107/PE22
Rv2814c/-	(cc=0.5308)	info on Rv2814c/-
Rv2479c/-	(cc=0.5303)	info on Rv2479c/-
Rv2106/-	(cc=0.5263)	info on Rv2106/-

Correlation of Rv1196/PPE18 with Rv2479c/-

Normalized LFCs for Rv1196/PPE18:
(description and provenance of datasets)

	Rv1196/PPE18	Rv2479c/-
Fe_supp_jason_reseq	-0.06	-0.535
low_pH_jason_reseq	-1.091	-0.529
NO_jason_reseq	-0.914	-0.15
B6_jason_reseq	-1.217	-0.465
MHCII_jason_reseq	0.228	-0.222
Isoniazid02	2.462	-0.09
Rifampicin4	0.842	0.782
Ethambutol3	1.445	0.507
Meropenem3	-0.121	-0.24
Vancomycin16	0.531	-0.196
Rv2680_day32	-1.276	0.27
H37Rv_KO_MarP	-0.934	-0.188
hypoxia_3wks	0.626	0.459
hypoxia_6wks	0.875	0.063
glycerol	0.828	-0.543
cholesterol	0.379	0.151
AJ	1.657	1.467
Bibs02	0.685	1.211
Bibs02c	1.155	1.878
BL6	1.282	0.362
BL6a	1.591	1.179
BXD01	0.97	0.748
BXD010	0.644	1.05
BXD011	1.367	0.984
BXD03	1.557	0.814
BXD04	0.999	0.671
BXD05	1.494	1.219
BXD06	0.919	0.659
BXD07	0.923	0.867
BXD08	1.004	0.595
BXD09	1.004	0.812
CAST	0.863	1.51
CCcont	1.275	0.356
DS01	1.246	1.237
DS02	0.892	1.123
DS04	1.684	1.37
DS0c	1.171	1.292
GP01	0.765	1.356
GP02	0.418	1.464
GP0c	0.506	0.962
NOD	0.133	1.572
NZO	0.761	1.269
PWK	0.999	1.468
H37Rv_KO_CtpC	-0.175	1.011
H37Rv_KO_CtpD	1.298	0.925
H37Rv_KO_Rv1272	1.113	0.739
H37Rv_KO_SugABC	1.499	0.917
H37Rv_KO_MbtN	1.065	0.659
Trans05	0.993	1.013
macrophage_unactivated	0.246	-0.814
IL1	-1.16	-0.765
Rapamycin	-0.35	-1.132
Tcell	-1.0	-1.714
GMCSF	-0.742	-0.581
IFNab	1.62	-1.04
IFNg	-1.868	-0.711
IFNg_GMCSF1	-0.308	-0.355
Rv1432_day32	-0.271	0.378
Rv1565c_day32	-0.101	0.145
secA2_input	-0.312	0.18
delta_Rv3594	0.569	0.093
delta_Rv3717	0.865	-0.034
delta_Rv3811	0.758	0.0
delta_Rv0954	0.339	0.553
PonA1	-0.369	-0.021
EccD1_KO	0.122	0.151
EspI_KO	1.32	0.799
PE35_KO	0.72	0.796
PPE68_KO	0.157	0.557
glycerol2	1.103	-0.733
lignocerate	0.742	-0.438
oleate	-0.425	-0.829
phosphatidylcholine	1.064	-0.648
acetate	-0.045	0.035
glucAc	0.176	0.179
Rv0950ko	-0.057	0.081
Rv1096ko	-0.03	0.081
Rv3684ko	-0.226	-0.596
delta_otsA_trehalose	1.263	0.083