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 Rv1452c/PE_PGRS28:

update plot	correlation	link to info on gene
Rv0336/-	(cc=0.5509)	info on Rv0336/-
Rv1450c/PE_PGRS27	(cc=0.548)	info on Rv1450c/PE_PGRS27
Rv0833/PE_PGRS13	(cc=0.5475)	info on Rv0833/PE_PGRS13
Rv1067c/PE_PGRS19	(cc=0.5443)	info on Rv1067c/PE_PGRS19
Rv2649/-	(cc=0.5406)	info on Rv2649/-
Rv3507/PE_PGRS53	(cc=0.5389)	info on Rv3507/PE_PGRS53
Rv1759c/wag22	(cc=0.5333)	info on Rv1759c/wag22
Rv2355/-	(cc=0.5299)	info on Rv2355/-
Rv1756c/-	(cc=0.5276)	info on Rv1756c/-
Rv1004c/-	(cc=0.523)	info on Rv1004c/-

Correlation of Rv1452c/PE_PGRS28 with Rv0336/-

Normalized LFCs for Rv1452c/PE_PGRS28:
(description and provenance of datasets)

	Rv1452c/PE_PGRS28	Rv0336/-
Fe_supp_jason_reseq	-0.046	0.0
low_pH_jason_reseq	-0.765	-1.445
NO_jason_reseq	-0.396	0.221
B6_jason_reseq	-0.24	-0.394
MHCII_jason_reseq	0.75	0.203
Isoniazid02	1.064	0.074
Rifampicin4	0.636	0.685
Ethambutol3	0.911	0.111
Meropenem3	1.12	0.601
Vancomycin16	0.027	0.207
Rv2680_day32	-0.669	-0.097
H37Rv_KO_MarP	-0.555	-0.025
hypoxia_3wks	0.0	0.267
hypoxia_6wks	-0.411	-0.361
glycerol	1.849	-0.079
cholesterol	0.649	0.043
AJ	1.04	0.553
Bibs02	1.558	0.562
Bibs02c	1.122	0.934
BL6	0.057	-0.042
BL6a	0.462	0.4
BXD01	0.149	0.064
BXD010	-0.125	0.131
BXD011	0.306	-0.161
BXD03	0.132	0.355
BXD04	0.1	0.501
BXD05	0.667	0.286
BXD06	-0.187	-0.07
BXD07	0.323	0.103
BXD08	0.34	0.146
BXD09	0.039	0.008
CAST	0.719	0.532
CCcont	-0.325	-0.184
DS01	0.31	0.662
DS02	0.474	0.233
DS04	1.313	0.49
DS0c	-0.041	0.149
GP01	0.825	0.475
GP02	1.219	0.591
GP0c	1.25	0.068
NOD	1.396	0.472
NZO	0.595	0.485
PWK	0.192	0.821
H37Rv_KO_CtpC	0.993	0.905
H37Rv_KO_CtpD	1.665	0.604
H37Rv_KO_Rv1272	-0.095	0.296
H37Rv_KO_SugABC	0.531	0.205
H37Rv_KO_MbtN	0.843	0.534
Trans05	0.095	0.455
macrophage_unactivated	-0.028	-0.603
IL1	0.05	-0.581
Rapamycin	-0.276	-0.503
Tcell	-0.74	-1.098
GMCSF	0.734	-0.164
IFNab	-0.656	-1.037
IFNg	-0.048	-0.246
IFNg_GMCSF1	-0.057	-0.242
Rv1432_day32	0.754	0.269
Rv1565c_day32	-0.635	0.028
secA2_input	-0.653	-0.034
delta_Rv3594	-0.217	-0.785
delta_Rv3717	0.477	-0.686
delta_Rv3811	-0.125	-0.781
delta_Rv0954	-0.667	-0.853
PonA1	-0.299	-0.488
EccD1_KO	0.724	-0.181
EspI_KO	-0.345	0.06
PE35_KO	0.079	0.093
PPE68_KO	-0.202	-0.022
glycerol2	-0.581	0.0
lignocerate	-0.567	0.116
oleate	-0.345	-0.136
phosphatidylcholine	-0.164	0.014
acetate	-0.982	-0.043
glucAc	0.026	0.308
Rv0950ko	0.042	0.398
Rv1096ko	0.223	0.012
Rv3684ko	-0.255	0.354
delta_otsA_trehalose	-1.019	0.144