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 Rv0832/PE_PGRS12

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

	Rv3351c/-	Rv0832/PE_PGRS12
Fe_supp_jason_reseq	-0.014	0.893
low_pH_jason_reseq	-0.36	0.157
NO_jason_reseq	-0.108	0.588
B6_jason_reseq	-0.684	-0.283
MHCII_jason_reseq	0.108	0.969
Isoniazid02	-0.282	-0.423
Rifampicin4	-0.366	0.726
Ethambutol3	0.435	-0.694
Meropenem3	0.28	-0.854
Vancomycin16	-0.316	-0.432
Rv2680_day32	0.504	-0.461
H37Rv_KO_MarP	0.296	0.196
hypoxia_3wks	0.187	0.283
hypoxia_6wks	0.263	-0.522
glycerol	0.17	1.454
cholesterol	0.084	4.229
AJ	0.588	0.899
Bibs02	0.295	0.523
Bibs02c	0.717	1.805
BL6	0.165	0.217
BL6a	0.283	1.834
BXD01	0.175	1.022
BXD010	-0.481	-0.01
BXD011	-0.239	0.38
BXD03	0.167	0.887
BXD04	-0.105	0.662
BXD05	0.408	1.347
BXD06	0.15	0.044
BXD07	0.112	-0.222
BXD08	0.673	1.001
BXD09	-0.009	0.101
CAST	0.207	1.697
CCcont	0.125	1.148
DS01	0.144	1.083
DS02	0.63	0.608
DS04	0.63	2.819
DS0c	0.848	1.994
GP01	-0.262	0.04
GP02	0.262	1.222
GP0c	-0.273	0.093
NOD	-0.145	0.037
NZO	0.173	0.795
PWK	0.078	1.08
H37Rv_KO_CtpC	0.318	1.487
H37Rv_KO_CtpD	1.464	1.763
H37Rv_KO_Rv1272	0.539	1.149
H37Rv_KO_SugABC	0.413	0.676
H37Rv_KO_MbtN	0.243	0.462
Trans05	0.063	0.835
macrophage_unactivated	0.038	0.947
IL1	-0.24	-0.795
Rapamycin	-0.181	-0.083
Tcell	0.147	-0.345
GMCSF	0.293	0.359
IFNab	0.426	0.082
IFNg	0.088	-0.11
IFNg_GMCSF1	0.167	-0.355
Rv1432_day32	0.445	0.256
Rv1565c_day32	0.028	-0.82
secA2_input	-0.319	0.512
delta_Rv3594	0.314	-0.315
delta_Rv3717	0.033	-0.042
delta_Rv3811	0.226	-0.251
delta_Rv0954	-0.277	-1.299
PonA1	0.035	0.013
EccD1_KO	-0.283	-0.437
EspI_KO	0.108	-0.662
PE35_KO	-0.055	-0.928
PPE68_KO	0.035	-0.877
glycerol2	0.391	0.552
lignocerate	0.431	-0.134
oleate	0.449	1.266
phosphatidylcholine	0.286	0.59
acetate	-0.086	-0.851
glucAc	-0.171	-1.108
Rv0950ko	0.25	-0.229
Rv1096ko	-0.347	-0.196
Rv3684ko	0.0	-0.855
delta_otsA_trehalose	-0.698	-0.195