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 Rv3454/-:

update plot	correlation	link to info on gene
Rv0159c/PE3	(cc=0.5515)	info on Rv0159c/PE3
Rv0028/-	(cc=0.5224)	info on Rv0028/-
Rv3885c/eccE2	(cc=0.5204)	info on Rv3885c/eccE2
Rv2584c/apt	(cc=0.5101)	info on Rv2584c/apt
Rv0059/-	(cc=0.5066)	info on Rv0059/-
Rv1664/pks9	(cc=0.488)	info on Rv1664/pks9
Rv2113/-	(cc=0.4807)	info on Rv2113/-
Rv3218/-	(cc=0.479)	info on Rv3218/-
Rv3524/-	(cc=0.4776)	info on Rv3524/-
Rv1021/-	(cc=0.4743)	info on Rv1021/-

Correlation of Rv3454/- with Rv0159c/PE3

Normalized LFCs for Rv3454/-:
(description and provenance of datasets)

	Rv3454/-	Rv0159c/PE3
Fe_supp_jason_reseq	0.57	0.489
low_pH_jason_reseq	-0.196	-0.515
NO_jason_reseq	-0.378	-0.165
B6_jason_reseq	-0.057	0.378
MHCII_jason_reseq	0.182	0.273
Isoniazid02	-0.258	-1.23
Rifampicin4	-0.076	0.138
Ethambutol3	0.151	-0.674
Meropenem3	-0.468	0.29
Vancomycin16	-0.175	-0.523
Rv2680_day32	0.307	0.421
H37Rv_KO_MarP	0.81	0.096
hypoxia_3wks	0.562	-0.371
hypoxia_6wks	1.023	-0.33
glycerol	-0.726	-0.227
cholesterol	-0.621	-0.35
AJ	0.25	-0.403
Bibs02	0.502	0.185
Bibs02c	0.117	0.006
BL6	0.768	0.374
BL6a	0.683	0.029
BXD01	0.367	0.482
BXD010	1.088	0.334
BXD011	0.531	0.398
BXD03	0.59	0.232
BXD04	1.458	0.666
BXD05	0.57	0.303
BXD06	0.442	0.351
BXD07	0.596	0.234
BXD08	0.384	0.473
BXD09	0.586	0.024
CAST	-0.135	0.24
CCcont	0.555	0.416
DS01	0.216	-0.05
DS02	0.532	0.244
DS04	0.037	-0.309
DS0c	0.464	-0.354
GP01	0.443	0.707
GP02	-0.083	0.599
GP0c	0.551	0.089
NOD	-0.319	0.539
NZO	0.25	-0.121
PWK	0.806	0.045
H37Rv_KO_CtpC	0.189	0.359
H37Rv_KO_CtpD	2.036	0.905
H37Rv_KO_Rv1272	0.387	0.516
H37Rv_KO_SugABC	1.622	0.492
H37Rv_KO_MbtN	-0.442	0.06
Trans05	-0.103	0.465
macrophage_unactivated	0.811	0.821
IL1	0.807	2.287
Rapamycin	1.046	2.087
Tcell	-0.951	-3.904
GMCSF	1.655	1.859
IFNab	1.17	1.868
IFNg	1.272	2.106
IFNg_GMCSF1	0.672	2.225
Rv1432_day32	0.837	0.578
Rv1565c_day32	-0.261	-0.131
secA2_input	-0.429	0.085
delta_Rv3594	-0.448	-0.072
delta_Rv3717	-0.215	-0.165
delta_Rv3811	0.067	0.043
delta_Rv0954	0.074	0.195
PonA1	-0.054	-0.173
EccD1_KO	-0.099	-0.428
EspI_KO	0.14	-0.419
PE35_KO	-0.4	-0.551
PPE68_KO	-0.064	-0.65
glycerol2	-0.31	1.033
lignocerate	-0.135	0.894
oleate	-0.481	0.749
phosphatidylcholine	-0.171	0.695
acetate	0.156	0.12
glucAc	-0.062	-0.038
Rv0950ko	-0.084	0.485
Rv1096ko	-0.35	-0.507
Rv3684ko	0.573	0.0
delta_otsA_trehalose	1.068	1.592