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 Rv3897c/-

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

	Rv2123/PPE37	Rv3897c/-
Fe_supp_jason_reseq	-0.702	0.082
low_pH_jason_reseq	-0.51	-0.552
NO_jason_reseq	0.05	-1.257
B6_jason_reseq	-0.184	0.291
MHCII_jason_reseq	0.434	0.249
Isoniazid02	-0.3	0.07
Rifampicin4	0.333	0.785
Ethambutol3	-0.531	0.502
Meropenem3	1.005	0.806
Vancomycin16	-0.334	0.345
Rv2680_day32	0.916	2.136
H37Rv_KO_MarP	-0.241	0.313
hypoxia_3wks	-0.056	-0.754
hypoxia_6wks	0.535	-0.307
glycerol	0.083	0.96
cholesterol	-0.583	0.497
AJ	0.24	1.434
Bibs02	-0.951	1.359
Bibs02c	0.685	1.761
BL6	-0.332	0.482
BL6a	0.485	0.558
BXD01	-0.102	0.25
BXD010	-0.795	0.253
BXD011	-0.31	-0.312
BXD03	0.044	0.03
BXD04	-0.825	-0.137
BXD05	-0.218	-0.849
BXD06	-0.116	0.133
BXD07	-0.146	-0.3
BXD08	-0.045	-0.62
BXD09	-0.149	-0.469
CAST	0.39	0.339
CCcont	-0.601	0.259
DS01	0.209	0.253
DS02	0.274	1.174
DS04	1.183	0.59
DS0c	0.071	-0.277
GP01	0.921	0.834
GP02	0.723	1.263
GP0c	0.618	0.48
NOD	0.444	0.286
NZO	0.129	0.799
PWK	-0.189	0.519
H37Rv_KO_CtpC	-0.201	-0.049
H37Rv_KO_CtpD	-0.406	-0.262
H37Rv_KO_Rv1272	0.546	0.347
H37Rv_KO_SugABC	0.492	0.126
H37Rv_KO_MbtN	-0.428	0.111
Trans05	0.404	1.091
macrophage_unactivated	-0.48	-1.174
IL1	-0.581	-1.634
Rapamycin	-0.792	-0.273
Tcell	-0.544	-1.14
GMCSF	0.333	0.024
IFNab	-0.121	-0.16
IFNg	-0.732	-1.179
IFNg_GMCSF1	-0.082	-0.899
Rv1432_day32	0.145	0.375
Rv1565c_day32	0.021	-0.199
secA2_input	0.614	1.019
delta_Rv3594	0.6	0.228
delta_Rv3717	0.401	0.263
delta_Rv3811	0.134	0.503
delta_Rv0954	0.05	-0.456
PonA1	1.192	0.287
EccD1_KO	1.131	1.128
EspI_KO	0.428	-0.077
PE35_KO	0.306	0.172
PPE68_KO	0.41	0.208
glycerol2	0.195	0.856
lignocerate	0.404	1.299
oleate	0.238	0.133
phosphatidylcholine	0.373	0.668
acetate	0.027	1.219
glucAc	0.188	1.534
Rv0950ko	1.04	1.785
Rv1096ko	1.074	1.984
Rv3684ko	0.095	1.402
delta_otsA_trehalose	0.596	-0.623