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 Rv1705c/PPE22:

update plot	correlation	link to info on gene
Rv1992c/ctpG	(cc=0.5366)	info on Rv1992c/ctpG
Rv0865/mog	(cc=0.5119)	info on Rv0865/mog
Rv2629/-	(cc=0.505)	info on Rv2629/-
Rv1233c/-	(cc=0.4996)	info on Rv1233c/-
Rv2226/-	(cc=0.4987)	info on Rv2226/-
Rv2784c/lppU	(cc=0.4638)	info on Rv2784c/lppU
Rv1280c/oppA	(cc=0.4549)	info on Rv1280c/oppA
Rv2725c/hflX	(cc=0.4525)	info on Rv2725c/hflX
Rv1878/glnA3	(cc=0.4443)	info on Rv1878/glnA3
Rv2089c/pepE	(cc=0.4435)	info on Rv2089c/pepE

Correlation of Rv1705c/PPE22 with Rv1233c/-

Normalized LFCs for Rv1705c/PPE22:
(description and provenance of datasets)

	Rv1705c/PPE22	Rv1233c/-
Fe_supp_jason_reseq	-0.568	-0.109
low_pH_jason_reseq	-1.029	-0.905
NO_jason_reseq	0.068	0.257
B6_jason_reseq	-0.727	-0.581
MHCII_jason_reseq	-0.418	-0.406
Isoniazid02	1.358	0.604
Rifampicin4	0.127	-0.162
Ethambutol3	0.745	-0.396
Meropenem3	1.846	1.559
Vancomycin16	0.244	-0.451
Rv2680_day32	0.152	0.18
H37Rv_KO_MarP	0.377	1.043
hypoxia_3wks	0.0	-0.171
hypoxia_6wks	-0.217	-0.773
glycerol	0.076	0.072
cholesterol	0.143	0.419
AJ	0.145	-0.313
Bibs02	-0.134	-0.283
Bibs02c	0.558	0.518
BL6	-0.2	-0.234
BL6a	0.23	0.433
BXD01	-0.478	0.455
BXD010	-0.326	0.788
BXD011	-0.345	0.738
BXD03	-0.137	-0.012
BXD04	0.33	0.107
BXD05	-0.127	0.487
BXD06	-0.553	0.76
BXD07	-0.307	0.037
BXD08	-0.043	0.19
BXD09	-0.153	0.223
CAST	-0.137	-0.285
CCcont	-0.38	0.359
DS01	-0.24	0.517
DS02	0.536	-0.734
DS04	1.072	0.261
DS0c	0.289	0.344
GP01	-0.318	0.141
GP02	-0.939	0.362
GP0c	-0.408	-0.918
NOD	0.412	0.303
NZO	-0.052	-0.438
PWK	-0.3	-0.304
H37Rv_KO_CtpC	0.131	0.447
H37Rv_KO_CtpD	0.868	0.392
H37Rv_KO_Rv1272	0.235	0.145
H37Rv_KO_SugABC	0.931	1.158
H37Rv_KO_MbtN	0.155	-0.31
Trans05	-0.929	-0.559
macrophage_unactivated	0.193	0.473
IL1	0.113	0.786
Rapamycin	-0.074	0.0
Tcell	0.437	0.306
GMCSF	0.729	0.805
IFNab	0.094	0.109
IFNg	0.043	0.0
IFNg_GMCSF1	-0.101	0.33
Rv1432_day32	0.082	0.571
Rv1565c_day32	0.262	0.539
secA2_input	0.081	0.188
delta_Rv3594	0.32	0.62
delta_Rv3717	0.028	0.877
delta_Rv3811	0.583	0.668
delta_Rv0954	0.451	1.05
PonA1	1.012	1.273
EccD1_KO	0.122	0.72
EspI_KO	0.131	1.192
PE35_KO	0.464	0.732
PPE68_KO	0.586	0.768
glycerol2	-0.073	-0.482
lignocerate	0.212	-0.234
oleate	0.196	0.306
phosphatidylcholine	0.332	0.018
acetate	-0.472	-0.702
glucAc	-0.122	0.067
Rv0950ko	0.404	0.166
Rv1096ko	-0.332	0.133
Rv3684ko	-0.029	-0.462
delta_otsA_trehalose	0.0	0.573