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 Rv3351c/-:

update plot	correlation	link to info on gene
Rv0072/-	(cc=0.4804)	info on Rv0072/-
Rv0305c/PPE6	(cc=0.4753)	info on Rv0305c/PPE6
Rv2665/-	(cc=0.4546)	info on Rv2665/-
Rv1948c/-	(cc=0.4485)	info on Rv1948c/-
Rv3440c/-	(cc=0.4421)	info on Rv3440c/-
Rv1145/mmpL13a	(cc=0.4416)	info on Rv1145/mmpL13a
Rv0832/PE_PGRS12	(cc=0.4345)	info on Rv0832/PE_PGRS12
Rv0194/-	(cc=0.4315)	info on Rv0194/-
Rv0138/-	(cc=0.431)	info on Rv0138/-
Rv2436/rbsK	(cc=0.4277)	info on Rv2436/rbsK

Correlation of Rv3351c/- with Rv0194/-

Normalized LFCs for Rv3351c/-:
(description and provenance of datasets)

	Rv3351c/-	Rv0194/-
Fe_supp_jason_reseq	-0.014	-0.058
low_pH_jason_reseq	-0.36	-0.393
NO_jason_reseq	-0.108	0.037
B6_jason_reseq	-0.684	-0.047
MHCII_jason_reseq	0.108	-0.046
Isoniazid02	-0.282	-0.858
Rifampicin4	-0.366	0.203
Ethambutol3	0.435	-0.409
Meropenem3	0.28	-1.028
Vancomycin16	-0.316	-0.464
Rv2680_day32	0.504	0.181
H37Rv_KO_MarP	0.296	0.456
hypoxia_3wks	0.187	0.056
hypoxia_6wks	0.263	0.115
glycerol	0.17	0.0
cholesterol	0.084	-0.104
AJ	0.588	0.111
Bibs02	0.295	0.0
Bibs02c	0.717	0.035
BL6	0.165	0.133
BL6a	0.283	0.089
BXD01	0.175	-0.121
BXD010	-0.481	0.049
BXD011	-0.239	0.049
BXD03	0.167	-0.036
BXD04	-0.105	0.234
BXD05	0.408	-0.11
BXD06	0.15	0.076
BXD07	0.112	0.159
BXD08	0.673	0.043
BXD09	-0.009	-0.027
CAST	0.207	0.067
CCcont	0.125	-0.01
DS01	0.144	-0.046
DS02	0.63	0.071
DS04	0.63	0.056
DS0c	0.848	0.481
GP01	-0.262	0.584
GP02	0.262	0.367
GP0c	-0.273	-0.07
NOD	-0.145	0.164
NZO	0.173	0.498
PWK	0.078	0.266
H37Rv_KO_CtpC	0.318	0.053
H37Rv_KO_CtpD	1.464	1.262
H37Rv_KO_Rv1272	0.539	-0.274
H37Rv_KO_SugABC	0.413	0.454
H37Rv_KO_MbtN	0.243	0.423
Trans05	0.063	0.303
macrophage_unactivated	0.038	-0.016
IL1	-0.24	-0.131
Rapamycin	-0.181	-0.193
Tcell	0.147	-0.339
GMCSF	0.293	0.063
IFNab	0.426	0.115
IFNg	0.088	0.051
IFNg_GMCSF1	0.167	0.148
Rv1432_day32	0.445	0.194
Rv1565c_day32	0.028	-0.469
secA2_input	-0.319	0.025
delta_Rv3594	0.314	-0.304
delta_Rv3717	0.033	-0.214
delta_Rv3811	0.226	-0.173
delta_Rv0954	-0.277	-0.275
PonA1	0.035	-0.54
EccD1_KO	-0.283	-0.168
EspI_KO	0.108	-0.362
PE35_KO	-0.055	-0.519
PPE68_KO	0.035	-0.518
glycerol2	0.391	0.61
lignocerate	0.431	0.496
oleate	0.449	0.564
phosphatidylcholine	0.286	0.335
acetate	-0.086	0.098
glucAc	-0.171	-0.025
Rv0950ko	0.25	0.507
Rv1096ko	-0.347	-0.341
Rv3684ko	0.0	0.0
delta_otsA_trehalose	-0.698	-0.205