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 Rv2712c/-:

update plot	correlation	link to info on gene
Rv3906c/-	(cc=0.5133)	info on Rv3906c/-
Rv0325/-	(cc=0.506)	info on Rv0325/-
Rv2020c/-	(cc=0.4764)	info on Rv2020c/-
Rv1688/mpg	(cc=0.4674)	info on Rv1688/mpg
Rv2238c/ahpE	(cc=0.4601)	info on Rv2238c/ahpE
Rv2629/-	(cc=0.4594)	info on Rv2629/-
Rv0735/sigL	(cc=0.4409)	info on Rv0735/sigL
Rv0747/PE_PGRS10	(cc=0.4391)	info on Rv0747/PE_PGRS10
Rv1378c/-	(cc=0.4338)	info on Rv1378c/-
Rv1442/bisC	(cc=0.4318)	info on Rv1442/bisC

Correlation of Rv2712c/- with Rv0747/PE_PGRS10

Normalized LFCs for Rv2712c/-:
(description and provenance of datasets)

	Rv2712c/-	Rv0747/PE_PGRS10
Fe_supp_jason_reseq	-0.046	-0.48
low_pH_jason_reseq	0.4	0.709
NO_jason_reseq	0.407	-0.247
B6_jason_reseq	-0.54	0.173
MHCII_jason_reseq	0.617	0.941
Isoniazid02	1.487	0.064
Rifampicin4	0.157	0.233
Ethambutol3	0.969	0.37
Meropenem3	0.424	2.002
Vancomycin16	0.393	-0.456
Rv2680_day32	-0.083	-0.171
H37Rv_KO_MarP	-0.697	0.027
hypoxia_3wks	-0.395	0.243
hypoxia_6wks	0.207	0.127
glycerol	0.619	1.924
cholesterol	0.377	1.091
AJ	0.469	1.866
Bibs02	0.499	0.993
Bibs02c	-0.482	1.223
BL6	-0.561	-1.133
BL6a	-0.677	0.092
BXD01	0.042	-0.476
BXD010	-0.847	-0.958
BXD011	-0.236	-0.651
BXD03	-0.403	-0.495
BXD04	-0.368	0.014
BXD05	-0.132	-0.687
BXD06	-0.136	-0.845
BXD07	-0.231	-0.629
BXD08	-0.171	-0.556
BXD09	-0.144	-0.587
CAST	0.01	0.786
CCcont	-0.553	-0.733
DS01	0.228	0.188
DS02	0.38	0.569
DS04	-0.287	0.134
DS0c	-0.321	0.335
GP01	-0.631	-0.814
GP02	0.535	0.17
GP0c	0.077	-0.498
NOD	-0.189	0.415
NZO	0.342	0.503
PWK	0.233	0.863
H37Rv_KO_CtpC	-0.718	-0.079
H37Rv_KO_CtpD	0.462	-0.341
H37Rv_KO_Rv1272	-0.499	-0.446
H37Rv_KO_SugABC	0.594	0.338
H37Rv_KO_MbtN	0.382	0.921
Trans05	-0.237	-0.434
macrophage_unactivated	-0.095	-0.518
IL1	0.154	-0.561
Rapamycin	-0.31	-1.531
Tcell	-0.225	-0.701
GMCSF	0.378	0.694
IFNab	0.514	-1.605
IFNg	-0.102	-1.334
IFNg_GMCSF1	0.321	0.069
Rv1432_day32	0.094	0.222
Rv1565c_day32	0.341	-1.524
secA2_input	-0.351	0.205
delta_Rv3594	0.207	-0.567
delta_Rv3717	-0.457	-0.657
delta_Rv3811	-0.055	-0.564
delta_Rv0954	-0.479	-1.978
PonA1	-0.196	-0.891
EccD1_KO	0.526	0.763
EspI_KO	0.365	-0.117
PE35_KO	-0.551	0.088
PPE68_KO	-0.378	0.096
glycerol2	0.161	0.464
lignocerate	0.622	0.615
oleate	0.736	0.469
phosphatidylcholine	0.655	0.564
acetate	0.336	0.785
glucAc	0.187	0.8
Rv0950ko	0.214	0.684
Rv1096ko	0.042	0.838
Rv3684ko	0.072	0.164
delta_otsA_trehalose	0.576	1.365