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 Rv2954c/-:

update plot	correlation	link to info on gene
Rv2345/-	(cc=0.5093)	info on Rv2345/-
Rv3323c/moaX	(cc=0.5085)	info on Rv3323c/moaX
Rv1981c/nrdF1	(cc=0.5056)	info on Rv1981c/nrdF1
Rv3164c/moxR3	(cc=0.5047)	info on Rv3164c/moxR3
Rv2675c/-	(cc=0.5015)	info on Rv2675c/-
Rv1175c/fadH	(cc=0.4701)	info on Rv1175c/fadH
Rv2429/ahpD	(cc=0.4693)	info on Rv2429/ahpD
Rv2602/vapC41	(cc=0.4588)	info on Rv2602/vapC41
Rv0940c/-	(cc=0.4577)	info on Rv0940c/-
Rv1511/gmdA	(cc=0.4575)	info on Rv1511/gmdA

Correlation of Rv2954c/- with Rv2345/-

Normalized LFCs for Rv2954c/-:
(description and provenance of datasets)

	Rv2954c/-	Rv2345/-
Fe_supp_jason_reseq	0.18	-0.019
low_pH_jason_reseq	-1.161	-0.962
NO_jason_reseq	-0.412	-0.053
B6_jason_reseq	-0.145	-0.063
MHCII_jason_reseq	-0.033	0.065
Isoniazid02	-0.723	-1.199
Rifampicin4	0.241	0.509
Ethambutol3	-0.405	-1.019
Meropenem3	-0.68	-1.409
Vancomycin16	-0.17	-0.655
Rv2680_day32	0.205	-0.466
H37Rv_KO_MarP	-0.069	-0.02
hypoxia_3wks	-0.104	0.032
hypoxia_6wks	0.052	0.257
glycerol	0.439	0.192
cholesterol	-0.029	-0.086
AJ	-0.123	0.0
Bibs02	-0.449	-0.278
Bibs02c	-0.631	-0.205
BL6	0.216	0.138
BL6a	0.263	0.118
BXD01	0.268	0.14
BXD010	0.447	0.141
BXD011	0.468	-0.262
BXD03	0.66	-0.04
BXD04	0.546	0.291
BXD05	0.644	0.374
BXD06	0.056	0.147
BXD07	0.194	0.238
BXD08	-0.063	0.434
BXD09	0.494	0.199
CAST	-0.053	-0.225
CCcont	0.171	0.024
DS01	-0.062	0.0
DS02	-0.169	-0.498
DS04	0.222	-0.142
DS0c	0.368	-0.057
GP01	1.056	0.277
GP02	-0.374	0.072
GP0c	-0.138	0.147
NOD	0.812	0.265
NZO	0.012	-0.237
PWK	0.347	-0.058
H37Rv_KO_CtpC	-0.465	0.373
H37Rv_KO_CtpD	0.501	0.605
H37Rv_KO_Rv1272	1.286	0.291
H37Rv_KO_SugABC	0.428	0.767
H37Rv_KO_MbtN	0.066	0.628
Trans05	0.423	0.501
macrophage_unactivated	-0.076	-0.114
IL1	-0.641	0.338
Rapamycin	0.055	0.473
Tcell	-0.394	0.039
GMCSF	-0.05	0.599
IFNab	-0.357	0.311
IFNg	0.206	0.216
IFNg_GMCSF1	1.178	0.182
Rv1432_day32	0.631	0.194
Rv1565c_day32	0.605	0.175
secA2_input	-0.775	0.233
delta_Rv3594	0.083	0.271
delta_Rv3717	-0.186	0.055
delta_Rv3811	0.311	0.352
delta_Rv0954	0.075	0.371
PonA1	0.5	-0.321
EccD1_KO	0.234	0.704
EspI_KO	0.482	0.767
PE35_KO	0.846	0.429
PPE68_KO	0.419	0.176
glycerol2	1.092	0.277
lignocerate	0.822	0.284
oleate	1.143	0.702
phosphatidylcholine	1.049	0.153
acetate	0.007	-0.462
glucAc	-0.026	-0.232
Rv0950ko	0.223	0.434
Rv1096ko	-0.63	-0.567
Rv3684ko	-0.082	-0.54
delta_otsA_trehalose	0.216	0.582