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 Rv2123/PPE37:

update plot	correlation	link to info on gene
Rv1527c/pks5	(cc=0.534)	info on Rv1527c/pks5
Rv1818c/PE_PGRS33	(cc=0.5296)	info on Rv1818c/PE_PGRS33
Rv1834/lipZ	(cc=0.5206)	info on Rv1834/lipZ
Rv1894c/-	(cc=0.516)	info on Rv1894c/-
Rv0577/TB27.3	(cc=0.5093)	info on Rv0577/TB27.3
Rv1735c/-	(cc=0.5002)	info on Rv1735c/-
Rv3897c/-	(cc=0.497)	info on Rv3897c/-
Rv2489c/-	(cc=0.4832)	info on Rv2489c/-
Rv2742c/-	(cc=0.4749)	info on Rv2742c/-
Rv2741/PE_PGRS47	(cc=0.4707)	info on Rv2741/PE_PGRS47

Correlation of Rv2123/PPE37 with Rv1527c/pks5

Normalized LFCs for Rv2123/PPE37:
(description and provenance of datasets)

	Rv2123/PPE37	Rv1527c/pks5
Fe_supp_jason_reseq	-0.702	0.175
low_pH_jason_reseq	-0.51	-0.587
NO_jason_reseq	0.05	-0.155
B6_jason_reseq	-0.184	0.181
MHCII_jason_reseq	0.434	0.229
Isoniazid02	-0.3	-0.015
Rifampicin4	0.333	-0.057
Ethambutol3	-0.531	0.225
Meropenem3	1.005	0.915
Vancomycin16	-0.334	-0.056
Rv2680_day32	0.916	-0.199
H37Rv_KO_MarP	-0.241	0.189
hypoxia_3wks	-0.056	0.159
hypoxia_6wks	0.535	0.294
glycerol	0.083	0.196
cholesterol	-0.583	0.013
AJ	0.24	0.622
Bibs02	-0.951	0.15
Bibs02c	0.685	0.477
BL6	-0.332	0.251
BL6a	0.485	0.066
BXD01	-0.102	-0.215
BXD010	-0.795	0.021
BXD011	-0.31	-0.262
BXD03	0.044	-0.108
BXD04	-0.825	-0.508
BXD05	-0.218	0.022
BXD06	-0.116	-0.39
BXD07	-0.146	-0.036
BXD08	-0.045	0.022
BXD09	-0.149	-0.304
CAST	0.39	-0.12
CCcont	-0.601	0.025
DS01	0.209	0.554
DS02	0.274	0.126
DS04	1.183	0.455
DS0c	0.071	0.325
GP01	0.921	1.712
GP02	0.723	0.477
GP0c	0.618	0.555
NOD	0.444	0.304
NZO	0.129	0.314
PWK	-0.189	-0.017
H37Rv_KO_CtpC	-0.201	0.314
H37Rv_KO_CtpD	-0.406	0.143
H37Rv_KO_Rv1272	0.546	0.415
H37Rv_KO_SugABC	0.492	0.611
H37Rv_KO_MbtN	-0.428	-0.13
Trans05	0.404	0.289
macrophage_unactivated	-0.48	-0.158
IL1	-0.581	-0.074
Rapamycin	-0.792	-0.114
Tcell	-0.544	-0.081
GMCSF	0.333	0.19
IFNab	-0.121	-0.151
IFNg	-0.732	-0.134
IFNg_GMCSF1	-0.082	0.189
Rv1432_day32	0.145	0.216
Rv1565c_day32	0.021	-0.104
secA2_input	0.614	0.523
delta_Rv3594	0.6	0.021
delta_Rv3717	0.401	-0.374
delta_Rv3811	0.134	0.312
delta_Rv0954	0.05	-0.172
PonA1	1.192	0.492
EccD1_KO	1.131	0.089
EspI_KO	0.428	0.262
PE35_KO	0.306	0.23
PPE68_KO	0.41	0.378
glycerol2	0.195	0.46
lignocerate	0.404	0.673
oleate	0.238	0.373
phosphatidylcholine	0.373	0.696
acetate	0.027	0.845
glucAc	0.188	0.441
Rv0950ko	1.04	0.422
Rv1096ko	1.074	0.311
Rv3684ko	0.095	0.498
delta_otsA_trehalose	0.596	0.551