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 Rv0086/hycQ:

update plot	correlation	link to info on gene
Rv0301/vapC2	(cc=0.4779)	info on Rv0301/vapC2
Rv0478/deoC	(cc=0.4737)	info on Rv0478/deoC
Rv2211c/gcvT	(cc=0.4671)	info on Rv2211c/gcvT
Rv1933c/fadE18	(cc=0.4588)	info on Rv1933c/fadE18
Rv2510c/-	(cc=0.4569)	info on Rv2510c/-
Rv0161/-	(cc=0.4453)	info on Rv0161/-
Rv2833c/ugpB	(cc=0.4347)	info on Rv2833c/ugpB
Rv1743/pknE	(cc=0.4318)	info on Rv1743/pknE
Rv3831/-	(cc=0.4233)	info on Rv3831/-
Rv1207/folP2	(cc=0.4214)	info on Rv1207/folP2

Correlation of Rv0086/hycQ with Rv0301/vapC2

Normalized LFCs for Rv0086/hycQ:
(description and provenance of datasets)

	Rv0086/hycQ	Rv0301/vapC2
Fe_supp_jason_reseq	0.128	0.107
low_pH_jason_reseq	-1.409	-0.716
NO_jason_reseq	-1.289	-0.31
B6_jason_reseq	-0.381	-0.563
MHCII_jason_reseq	-0.143	0.168
Isoniazid02	0.902	-0.351
Rifampicin4	0.187	-0.701
Ethambutol3	1.082	-0.513
Meropenem3	0.443	1.003
Vancomycin16	0.093	-0.106
Rv2680_day32	2.467	0.957
H37Rv_KO_MarP	0.545	0.24
hypoxia_3wks	0.817	-0.12
hypoxia_6wks	1.393	-0.071
glycerol	-0.563	-0.718
cholesterol	-0.033	-0.149
AJ	-1.171	-0.561
Bibs02	0.229	0.06
Bibs02c	-0.246	0.612
BL6	0.107	-0.021
BL6a	0.607	0.574
BXD01	0.986	0.614
BXD010	1.309	0.176
BXD011	1.415	0.591
BXD03	0.602	0.127
BXD04	0.587	0.576
BXD05	1.004	0.468
BXD06	0.317	0.323
BXD07	1.191	0.693
BXD08	0.79	0.55
BXD09	0.744	0.397
CAST	-0.105	0.357
CCcont	0.849	0.676
DS01	-0.053	0.243
DS02	0.592	0.726
DS04	0.084	0.1
DS0c	1.059	0.311
GP01	1.148	1.151
GP02	-0.621	0.787
GP0c	0.502	0.471
NOD	0.192	-0.408
NZO	-1.156	-0.212
PWK	-1.137	-0.139
H37Rv_KO_CtpC	0.035	-0.151
H37Rv_KO_CtpD	0.583	0.493
H37Rv_KO_Rv1272	-0.131	0.137
H37Rv_KO_SugABC	-1.33	0.367
H37Rv_KO_MbtN	-1.23	0.486
Trans05	1.864	0.521
macrophage_unactivated	0.0	0.638
IL1	1.32	0.466
Rapamycin	1.274	-0.074
Tcell	0.89	0.251
GMCSF	0.766	0.782
IFNab	0.46	1.442
IFNg	0.307	0.722
IFNg_GMCSF1	0.751	0.918
Rv1432_day32	-0.568	0.039
Rv1565c_day32	0.142	0.193
secA2_input	1.044	0.756
delta_Rv3594	-1.037	-1.398
delta_Rv3717	-0.853	-0.795
delta_Rv3811	-0.488	-0.696
delta_Rv0954	-0.536	-0.457
PonA1	-0.825	-0.26
EccD1_KO	0.973	0.53
EspI_KO	0.844	0.271
PE35_KO	0.0	-0.563
PPE68_KO	0.0	-0.502
glycerol2	-0.297	0.261
lignocerate	0.134	0.468
oleate	-0.468	-0.221
phosphatidylcholine	-0.244	0.197
acetate	0.106	0.341
glucAc	-0.452	0.531
Rv0950ko	-0.292	0.962
Rv1096ko	1.007	0.22
Rv3684ko	0.845	0.789
delta_otsA_trehalose	-0.459	0.404