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 Rv1042c/-:

update plot	correlation	link to info on gene
Rv1149/-	(cc=0.8949)	info on Rv1149/-
Rv1041c/-	(cc=0.6823)	info on Rv1041c/-
Rv1135c/PPE16	(cc=0.63)	info on Rv1135c/PPE16
Rv3144c/PPE52	(cc=0.4829)	info on Rv3144c/PPE52
Rv0540/-	(cc=0.4504)	info on Rv0540/-
Rv0578c/PE_PGRS7	(cc=0.4456)	info on Rv0578c/PE_PGRS7
Rv0546c/-	(cc=0.4453)	info on Rv0546c/-
Rv1071c/echA9	(cc=0.4413)	info on Rv1071c/echA9
Rv0621/-	(cc=0.4403)	info on Rv0621/-
Rv0755c/PPE12	(cc=0.4396)	info on Rv0755c/PPE12

Correlation of Rv1042c/- with Rv3144c/PPE52

Normalized LFCs for Rv1042c/-:
(description and provenance of datasets)

	Rv1042c/-	Rv3144c/PPE52
Fe_supp_jason_reseq	-1.46	-0.859
low_pH_jason_reseq	-1.064	-0.263
NO_jason_reseq	-0.78	-0.362
B6_jason_reseq	0.796	-0.381
MHCII_jason_reseq	0.763	-0.058
Isoniazid02	0.451	0.287
Rifampicin4	1.914	0.62
Ethambutol3	0.814	2.379
Meropenem3	0.994	0.478
Vancomycin16	1.292	0.255
Rv2680_day32	-0.571	-0.331
H37Rv_KO_MarP	-0.032	0.107
hypoxia_3wks	1.049	0.857
hypoxia_6wks	1.33	-0.023
glycerol	0.168	0.743
cholesterol	0.131	0.219
AJ	0.734	0.884
Bibs02	0.372	0.395
Bibs02c	1.84	1.249
BL6	-0.98	-0.56
BL6a	1.413	0.992
BXD01	-0.009	0.049
BXD010	0.413	0.786
BXD011	-0.323	0.139
BXD03	0.618	0.238
BXD04	-0.744	-0.192
BXD05	0.39	0.486
BXD06	0.075	0.224
BXD07	0.171	0.609
BXD08	-0.8	0.407
BXD09	0.32	0.078
CAST	0.692	0.833
CCcont	-1.018	-0.352
DS01	1.09	0.472
DS02	0.922	-0.151
DS04	0.188	0.606
DS0c	0.592	0.954
GP01	-2.405	0.465
GP02	-0.64	0.779
GP0c	-0.317	0.818
NOD	1.866	0.687
NZO	0.058	0.019
PWK	0.915	0.145
H37Rv_KO_CtpC	3.218	0.861
H37Rv_KO_CtpD	1.339	1.286
H37Rv_KO_Rv1272	0.01	0.819
H37Rv_KO_SugABC	-1.494	0.108
H37Rv_KO_MbtN	0.877	-0.573
Trans05	0.698	1.636
macrophage_unactivated	-1.932	-0.486
IL1	-0.033	-0.424
Rapamycin	0.034	0.187
Tcell	-0.551	-0.316
GMCSF	-0.383	0.135
IFNab	-0.692	0.124
IFNg	-1.187	0.0
IFNg_GMCSF1	-0.962	-0.342
Rv1432_day32	0.868	0.458
Rv1565c_day32	0.485	0.193
secA2_input	1.481	0.013
delta_Rv3594	0.239	0.199
delta_Rv3717	1.402	1.044
delta_Rv3811	0.824	0.323
delta_Rv0954	0.899	0.913
PonA1	-0.431	0.368
EccD1_KO	1.095	0.454
EspI_KO	1.315	-0.211
PE35_KO	1.423	0.615
PPE68_KO	1.689	0.758
glycerol2	-0.495	-0.325
lignocerate	-0.631	-0.462
oleate	-0.038	0.031
phosphatidylcholine	-0.242	-0.503
acetate	0.0	-0.811
glucAc	0.082	-0.627
Rv0950ko	0.597	0.555
Rv1096ko	1.252	0.259
Rv3684ko	-0.239	-0.239
delta_otsA_trehalose	-1.073	0.108