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 Rv2113/-:

update plot	correlation	link to info on gene
Rv0159c/PE3	(cc=0.856)	info on Rv0159c/PE3
Rv1817/-	(cc=0.8479)	info on Rv1817/-
Rv3815c/-	(cc=0.7418)	info on Rv3815c/-
Rv0453/PPE11	(cc=0.7248)	info on Rv0453/PPE11
Rv2848c/cobB	(cc=0.7197)	info on Rv2848c/cobB
Rv2822c/-	(cc=0.6508)	info on Rv2822c/-
Rv3685c/cyp137	(cc=0.5386)	info on Rv3685c/cyp137
Rv3862c/whiB6	(cc=0.5193)	info on Rv3862c/whiB6
Rv1021/-	(cc=0.4871)	info on Rv1021/-
Rv2339/mmpL9	(cc=0.4851)	info on Rv2339/mmpL9

Correlation of Rv2113/- with Rv2848c/cobB

Normalized LFCs for Rv2113/-:
(description and provenance of datasets)

	Rv2113/-	Rv2848c/cobB
Fe_supp_jason_reseq	0.922	0.66
low_pH_jason_reseq	-1.379	-0.212
NO_jason_reseq	-0.559	0.071
B6_jason_reseq	-1.249	0.274
MHCII_jason_reseq	-0.531	0.558
Isoniazid02	-1.043	1.521
Rifampicin4	0.406	0.72
Ethambutol3	0.657	1.454
Meropenem3	-0.462	0.187
Vancomycin16	-0.231	0.706
Rv2680_day32	-0.825	-0.633
H37Rv_KO_MarP	0.159	-0.161
hypoxia_3wks	-0.012	0.263
hypoxia_6wks	-0.568	-0.035
glycerol	0.237	0.426
cholesterol	-0.405	0.385
AJ	0.356	0.521
Bibs02	-0.372	0.534
Bibs02c	-0.209	0.303
BL6	0.418	0.39
BL6a	0.169	-0.034
BXD01	-0.106	-0.805
BXD010	-0.113	-1.385
BXD011	0.753	-0.787
BXD03	0.123	-0.372
BXD04	-0.166	-0.708
BXD05	0.301	-0.832
BXD06	0.224	-0.705
BXD07	0.171	-1.089
BXD08	0.265	-0.251
BXD09	0.103	-1.055
CAST	-0.828	0.02
CCcont	0.169	-0.497
DS01	-0.335	0.58
DS02	0.098	0.799
DS04	-0.218	0.748
DS0c	0.11	0.487
GP01	0.072	-0.741
GP02	-0.087	-0.257
GP0c	0.142	-0.167
NOD	-0.404	-0.334
NZO	-0.604	0.212
PWK	-0.409	0.342
H37Rv_KO_CtpC	0.148	-0.324
H37Rv_KO_CtpD	0.72	-0.067
H37Rv_KO_Rv1272	0.551	-0.372
H37Rv_KO_SugABC	1.132	-1.675
H37Rv_KO_MbtN	0.42	-1.399
Trans05	0.939	-0.419
macrophage_unactivated	1.143	2.071
IL1	2.886	2.948
Rapamycin	3.167	2.627
Tcell	-6.0	-4.822
GMCSF	2.756	2.986
IFNab	2.663	3.223
IFNg	2.905	2.881
IFNg_GMCSF1	2.963	4.342
Rv1432_day32	0.322	-0.257
Rv1565c_day32	1.531	0.134
secA2_input	0.128	1.061
delta_Rv3594	-0.337	-0.199
delta_Rv3717	-0.154	-0.273
delta_Rv3811	-0.312	-1.05
delta_Rv0954	0.181	-0.696
PonA1	-0.268	0.17
EccD1_KO	0.148	-0.122
EspI_KO	0.222	0.103
PE35_KO	-0.286	0.863
PPE68_KO	-0.147	0.39
glycerol2	0.894	0.475
lignocerate	0.616	0.66
oleate	1.331	0.2
phosphatidylcholine	0.999	0.675
acetate	0.342	1.714
glucAc	-0.082	0.59
Rv0950ko	0.25	-0.199
Rv1096ko	-0.13	0.507
Rv3684ko	-0.233	-1.068
delta_otsA_trehalose	0.537	0.322