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 Rv2088/pknJ:

update plot	correlation	link to info on gene
Rv0833/PE_PGRS13	(cc=0.5203)	info on Rv0833/PE_PGRS13
Rv1728c/-	(cc=0.4917)	info on Rv1728c/-
Rv1452c/PE_PGRS28	(cc=0.4782)	info on Rv1452c/PE_PGRS28
Rv3513c/fadD18	(cc=0.4742)	info on Rv3513c/fadD18
Rv2022c/-	(cc=0.4738)	info on Rv2022c/-
Rv3144c/PPE52	(cc=0.4645)	info on Rv3144c/PPE52
Rv1781c/malQ	(cc=0.4592)	info on Rv1781c/malQ
Rv1245c/-	(cc=0.4545)	info on Rv1245c/-
Rv3507/PE_PGRS53	(cc=0.4533)	info on Rv3507/PE_PGRS53
Rv1004c/-	(cc=0.453)	info on Rv1004c/-

Correlation of Rv2088/pknJ with Rv3144c/PPE52

Normalized LFCs for Rv2088/pknJ:
(description and provenance of datasets)

	Rv2088/pknJ	Rv3144c/PPE52
Fe_supp_jason_reseq	-0.822	-0.859
low_pH_jason_reseq	0.0	-0.263
NO_jason_reseq	-0.32	-0.362
B6_jason_reseq	-0.171	-0.381
MHCII_jason_reseq	0.479	-0.058
Isoniazid02	-0.02	0.287
Rifampicin4	0.463	0.62
Ethambutol3	-0.179	2.379
Meropenem3	0.307	0.478
Vancomycin16	0.584	0.255
Rv2680_day32	0.407	-0.331
H37Rv_KO_MarP	-0.522	0.107
hypoxia_3wks	0.73	0.857
hypoxia_6wks	-0.255	-0.023
glycerol	0.206	0.743
cholesterol	0.233	0.219
AJ	0.237	0.884
Bibs02	-0.101	0.395
Bibs02c	0.905	1.249
BL6	-0.555	-0.56
BL6a	0.386	0.992
BXD01	-0.187	0.049
BXD010	0.083	0.786
BXD011	-0.07	0.139
BXD03	-0.036	0.238
BXD04	-0.033	-0.192
BXD05	0.201	0.486
BXD06	0.275	0.224
BXD07	0.285	0.609
BXD08	-0.512	0.407
BXD09	0.193	0.078
CAST	0.782	0.833
CCcont	-0.757	-0.352
DS01	-0.339	0.472
DS02	-0.345	-0.151
DS04	0.659	0.606
DS0c	0.113	0.954
GP01	0.735	0.465
GP02	1.395	0.779
GP0c	0.209	0.818
NOD	0.807	0.687
NZO	-0.166	0.019
PWK	0.0	0.145
H37Rv_KO_CtpC	-0.022	0.861
H37Rv_KO_CtpD	0.829	1.286
H37Rv_KO_Rv1272	0.841	0.819
H37Rv_KO_SugABC	1.222	0.108
H37Rv_KO_MbtN	-0.458	-0.573
Trans05	0.698	1.636
macrophage_unactivated	-0.514	-0.486
IL1	-0.116	-0.424
Rapamycin	-0.632	0.187
Tcell	-0.531	-0.316
GMCSF	0.246	0.135
IFNab	-0.302	0.124
IFNg	-0.104	0.0
IFNg_GMCSF1	0.06	-0.342
Rv1432_day32	0.559	0.458
Rv1565c_day32	-0.09	0.193
secA2_input	-1.257	0.013
delta_Rv3594	0.635	0.199
delta_Rv3717	0.341	1.044
delta_Rv3811	0.287	0.323
delta_Rv0954	-0.394	0.913
PonA1	0.223	0.368
EccD1_KO	-0.51	0.454
EspI_KO	-0.171	-0.211
PE35_KO	-0.044	0.615
PPE68_KO	-0.048	0.758
glycerol2	-0.09	-0.325
lignocerate	-0.407	-0.462
oleate	0.384	0.031
phosphatidylcholine	0.0	-0.503
acetate	-0.427	-0.811
glucAc	-0.823	-0.627
Rv0950ko	0.326	0.555
Rv1096ko	0.953	0.259
Rv3684ko	0.403	-0.239
delta_otsA_trehalose	-1.715	0.108