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 Rv1878/glnA3

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

	Rv1705c/PPE22	Rv1878/glnA3
Fe_supp_jason_reseq	-0.568	-1.455
low_pH_jason_reseq	-1.029	-0.539
NO_jason_reseq	0.068	0.441
B6_jason_reseq	-0.727	-1.4
MHCII_jason_reseq	-0.418	-0.125
Isoniazid02	1.358	0.45
Rifampicin4	0.127	0.309
Ethambutol3	0.745	0.344
Meropenem3	1.846	0.658
Vancomycin16	0.244	-0.329
Rv2680_day32	0.152	-1.017
H37Rv_KO_MarP	0.377	0.054
hypoxia_3wks	0.0	-0.323
hypoxia_6wks	-0.217	-0.484
glycerol	0.076	-0.044
cholesterol	0.143	0.09
AJ	0.145	0.175
Bibs02	-0.134	0.96
Bibs02c	0.558	0.115
BL6	-0.2	-0.255
BL6a	0.23	-0.27
BXD01	-0.478	-0.484
BXD010	-0.326	0.062
BXD011	-0.345	-0.374
BXD03	-0.137	-0.11
BXD04	0.33	-0.447
BXD05	-0.127	-0.408
BXD06	-0.553	0.0
BXD07	-0.307	-0.368
BXD08	-0.043	-0.33
BXD09	-0.153	-0.439
CAST	-0.137	-0.205
CCcont	-0.38	-0.168
DS01	-0.24	0.33
DS02	0.536	0.523
DS04	1.072	0.306
DS0c	0.289	-0.314
GP01	-0.318	-0.765
GP02	-0.939	-0.585
GP0c	-0.408	-0.167
NOD	0.412	0.871
NZO	-0.052	0.069
PWK	-0.3	-0.205
H37Rv_KO_CtpC	0.131	-0.345
H37Rv_KO_CtpD	0.868	0.311
H37Rv_KO_Rv1272	0.235	1.006
H37Rv_KO_SugABC	0.931	-0.227
H37Rv_KO_MbtN	0.155	0.084
Trans05	-0.929	0.15
macrophage_unactivated	0.193	-0.114
IL1	0.113	-0.288
Rapamycin	-0.074	1.025
Tcell	0.437	-0.156
GMCSF	0.729	0.412
IFNab	0.094	0.565
IFNg	0.043	0.58
IFNg_GMCSF1	-0.101	-0.346
Rv1432_day32	0.082	0.83
Rv1565c_day32	0.262	-0.033
secA2_input	0.081	0.161
delta_Rv3594	0.32	0.534
delta_Rv3717	0.028	0.385
delta_Rv3811	0.583	0.137
delta_Rv0954	0.451	0.597
PonA1	1.012	-0.114
EccD1_KO	0.122	0.865
EspI_KO	0.131	0.254
PE35_KO	0.464	0.893
PPE68_KO	0.586	0.515
glycerol2	-0.073	-0.286
lignocerate	0.212	0.101
oleate	0.196	-0.625
phosphatidylcholine	0.332	-0.041
acetate	-0.472	-0.357
glucAc	-0.122	0.131
Rv0950ko	0.404	0.226
Rv1096ko	-0.332	-0.238
Rv3684ko	-0.029	-0.973
delta_otsA_trehalose	0.0	0.41