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 Rv3440c/-

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

	Rv3351c/-	Rv3440c/-
Fe_supp_jason_reseq	-0.014	-0.278
low_pH_jason_reseq	-0.36	-0.925
NO_jason_reseq	-0.108	-0.788
B6_jason_reseq	-0.684	-0.178
MHCII_jason_reseq	0.108	-0.112
Isoniazid02	-0.282	0.838
Rifampicin4	-0.366	0.85
Ethambutol3	0.435	0.817
Meropenem3	0.28	0.724
Vancomycin16	-0.316	0.517
Rv2680_day32	0.504	0.505
H37Rv_KO_MarP	0.296	-0.023
hypoxia_3wks	0.187	0.152
hypoxia_6wks	0.263	0.0
glycerol	0.17	0.758
cholesterol	0.084	0.088
AJ	0.588	0.615
Bibs02	0.295	0.668
Bibs02c	0.717	0.299
BL6	0.165	-0.197
BL6a	0.283	0.113
BXD01	0.175	0.243
BXD010	-0.481	-0.789
BXD011	-0.239	-1.159
BXD03	0.167	-0.563
BXD04	-0.105	0.079
BXD05	0.408	-0.97
BXD06	0.15	-0.476
BXD07	0.112	-0.377
BXD08	0.673	0.037
BXD09	-0.009	0.019
CAST	0.207	0.417
CCcont	0.125	-0.107
DS01	0.144	0.874
DS02	0.63	0.837
DS04	0.63	0.86
DS0c	0.848	0.701
GP01	-0.262	0.0
GP02	0.262	1.055
GP0c	-0.273	0.213
NOD	-0.145	0.181
NZO	0.173	0.811
PWK	0.078	0.244
H37Rv_KO_CtpC	0.318	0.537
H37Rv_KO_CtpD	1.464	0.796
H37Rv_KO_Rv1272	0.539	0.343
H37Rv_KO_SugABC	0.413	1.312
H37Rv_KO_MbtN	0.243	0.29
Trans05	0.063	0.018
macrophage_unactivated	0.038	-0.464
IL1	-0.24	-0.065
Rapamycin	-0.181	0.178
Tcell	0.147	-0.42
GMCSF	0.293	-0.293
IFNab	0.426	0.417
IFNg	0.088	0.222
IFNg_GMCSF1	0.167	0.101
Rv1432_day32	0.445	0.158
Rv1565c_day32	0.028	-0.316
secA2_input	-0.319	-0.124
delta_Rv3594	0.314	-0.285
delta_Rv3717	0.033	-0.643
delta_Rv3811	0.226	-0.223
delta_Rv0954	-0.277	-0.398
PonA1	0.035	-0.63
EccD1_KO	-0.283	-0.237
EspI_KO	0.108	-0.011
PE35_KO	-0.055	-0.061
PPE68_KO	0.035	-0.147
glycerol2	0.391	1.042
lignocerate	0.431	0.56
oleate	0.449	1.059
phosphatidylcholine	0.286	0.737
acetate	-0.086	0.17
glucAc	-0.171	-0.134
Rv0950ko	0.25	0.805
Rv1096ko	-0.347	0.434
Rv3684ko	0.0	0.694
delta_otsA_trehalose	-0.698	-0.583