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'''Here is the [http://homes.gersteinlab.org/people/nbhardwaj/Human_TFs_with_Intensity.xls list] with various gene names mapped.'''

'''Citation:''' Bhardwaj, N., Carson, M. B., Abyzov, A., Yan, K-K., Lu, H. and Gerstein M. B. (2010) Analysis of Combinatorial Regulation: Scaling of Partnerships between Regulators with the Number of Governed Targets, ''PLoS Comp Biol'' (in press).


'''Please read the following before using the file:'''

'''Why are there more than one entries sometime for one TF?'''

This list was compiled by cross-referencing various databases with other with BioMart as the main source.
Many of these databases don’t have one-to-one mapping for various TFs. So, I am listing all the mappings for each TF. That's there are many entries against one TF.
Probably, the primary reason for this is that the multiple entries are splice-variants of the same TF. Hence, multiple entries.


'''What does the first set of values indicate (Columns L through O)?'''

These values are the normalized values obtained by normalizing (using Quantile Normalization) across different *REPLICATES* in the same cell line.


'''Why are the values so different across different cell lines?'''

Bot much information is available about the sources of the experimental data, but we believe the conditions in which these values were obtained across different cell lines were different. For example, the experimental protocol, background settings, ways in which these intensity values were recorded, etc.
However, since we are mainly interested in the relative expression of these TFs *WITHIN* a cell line, difference in magnitude of the intensity values across these cell lines should not be a problem.
Nonetheless, a simple z-score fashion normalization across these cell lines was performed(see below for the next set of normalized values).


'''What do 1's and -'s indicate (Columns P through S)?'''

These just indicate if the TF is present (1) or absent (-) in a given cell line. Just to keep a count of how many cell lines a TF is present in.



'''What does the second set of values indicate (Columns T through W)?'''

These values are obtained by further normalizing each TF across different cell lines in a Z-score fashion. 
New value = (old value - Mean of the entire data)/Std Deviation of the entire data


'''How much can the Z-score fashion normalization be trusted?'''

Not much. These values from different cell lines are coming from experiments done prossibly under drastically different conditions in diff labs.
So, not sure how much sense does it make to do a z-score normalization.
Moreover, Z-score works best when the data follows normal distribution. This one probably doesn't.



'''Quick list of the TFs in Common name format.''' 

ABL1
ACTL6A
AFF3
AHR
AIRE
ALX1
ALX3
ALX4
APC
APEX1
AR
ARID3A
ARNT
ARNT2
ARNTL
ARNTL2
ATF1
ATF2
ATF3
ATF4
ATF5
ATF6
ATF7
ATOH1
BACH1
BACH2
BARHL2
BCL3
BCL6
BHLHB2
BHLHB3
BIN1
BNC1
BRCA1
BRCA2
BRIP1
BRPF1
CBFB
CCNH
CCNT1
CCNT2
CDC2
CDK2
CDK7
CDK9
CDX1
CDX2
CDX4
CEBPB
CEBPD
CEBPE
CEBPG
CEBPZ
CIITA
CLOCK
CREB1
CREB5
CREBBP
CRTC1
CRTC2
CRTC3
CRX
CSDA
CTBP1
CTCF
CTNNB1
CUTL1
CUTL2
DBP
DDB1
DDB2
DDIT3
DLX1
DLX2
DLX3
DLX4
DNMT1
DR1
E2F1
E2F2
E2F3
E2F4
E2F5
EGR1
EGR2
EGR3
EGR4
ELF1
ELF3
ELF5
ELK1
ELK3
ELK4
EMX2
EN1
EN2
EOMES
EP300
EPAS1
ERCC2
ERCC3
ERCC8
ERF
ERG
ESR1
ESR2
ESRRA
ESRRB
ESRRG
ETS1
ETS2
ETV1
ETV4
ETV5
ETV6
ETV7
EVI1
EVX1
EWSR1
EZH1
EZH2
FEV
FGF3
FKHL18
FLI1
FOS
FOSB
FOSL1
FOSL2
FOXA1
FOXA2
FOXA3
FOXB1
FOXC1
FOXC2
FOXD2
FOXD3
FOXD4
FOXE1
FOXE3
FOXF2
FOXG1
FOXH1
FOXI1
FOXJ1
FOXJ2
FOXJ3
FOXK2
FOXL1
FOXL2
FOXM1
FOXN3
FOXO1
FOXO3
FOXO4
FOXP1
FOXP2
FOXP3
FOXP4
FOXQ1
GABPA
GABPB2
GATA1
GATA2
GATA3
GATA4
GATA6
GBX1
GBX2
GCN5L2
GLI1
GLI3
GLIS2
GMEB1
GRHL1
GSC
GSCL
GTF2A1
GTF2A1L
GTF2A2
GTF2B
GTF2E1
GTF2E2
GTF2F1
GTF2F2
GTF2H1
GTF2H2
GTF2H3
GTF2I
GZF1
HAND1
HDAC1
HDAC2
HDAC3
HDAC4
HDAC5
HES1
HES2
HESX1
HEY1
HEY2
HEYL
HHEX
HIC1
HIF1A
HIVEP2
HLF
HLX
HMGA1
HMGB1
HMGB2
HNF1A
HNF1B
HNF4A
HNRNPA1
HOXA1
HOXA10
HOXA11
HOXA13
HOXA2
HOXA3
HOXA4
HOXA5
HOXA6
HOXA7
HOXA9
HOXB1
HOXB13
HOXB2
HOXB3
HOXB4
HOXB5
HOXB6
HOXB7
HOXB8
HOXB9
HOXC10
HOXC11
HOXC12
HOXC13
HOXC4
HOXC5
HOXC6
HOXC8
HOXC9
HOXD10
HOXD12
HOXD3
HOXD4
HOXD8
HOXD9
HSBP1
HSF1
HSF2
HSF4
ID1
ID2
ID3
IGFBP1
IKZF1
IKZF2
IKZF3
ING1
INSM1
IRF1
IRF2
IRF3
IRF4
IRF5
IRF6
IRF7
IRF8
IRF9
IRX2
IRX3
IRX4
IRX5
IRX6
JUN
JUNB
JUND
KCNIP1
KCNIP2
KCNIP3
KLF1
KLF10
KLF11
KLF12
KLF13
KLF15
KLF16
KLF2
KLF4
KLF5
KLF6
KLF7
KLF9
LBX1
LDB2
LEF1
LHX1
LHX2
LHX3
LHX4
LHX5
LITAF
LMO2
LMO3
LYL1
MAF
MAFA
MAFB
MAFF
MAFG
MAFK
MAML1
MAPK8IP1
MAZ
MECP2
MED21
MEF2A
MEF2B
MEF2C
MEF2D
MEIS1
MEOX1
MEOX2
MIXL1
MLL
MLX
MLXIP
MLXIPL
MNAT1
MNT
MNX1
MSC
MSX2
MTA2
MTF1
MXD1
MXI1
MYB
MYBBP1A
MYBL1
MYBL2
MYC
MYCBP
MYCL1
MYCN
MYF5
MYF6
MYOCD
MYOD1
MYOG
MYT1
MZF1
NAT10
NCOA1
NCOA2
NCOA3
NCOA6
NCOR1
NCOR2
NEUROD1
NEUROD2
NEUROG1
NEUROG3
NF1
NFAT5
NFATC2
NFATC3
NFATC4
NFE2
NFE2L1
NFE2L2
NFE2L3
NFIB
NFKB2
NFKBIA
NFKBIB
NFYA
NFYB
NHLH1
NHLH2
NKRF
NKX2-1
NKX2-2
NKX2-5
NKX2-8
NKX3-1
NKX3-2
NKX6-1
NKX6-2
NME2
NMI
NONO
NPAS1
NPAS2
NR0B1
NR0B2
NR1D1
NR1D2
NR1H2
NR1H3
NR1I2
NR2E1
NR2E3
NR2F1
NR2F2
NR2F6
NR3C1
NR3C2
NR4A1
NR4A2
NR4A3
NR5A1
NR5A2
NR6A1
NRF1
NRL
OLIG1
OLIG2
ONECUT1
ONECUT2
OTX1
OTX2
PAX1
PAX2
PAX3
PAX5
PAX6
PAX7
PAX8
PAX9
PBX1
PBX2
PBX2_HUMAN
PBX3
PCAF
PCGF2
PDX1
PFDN5
PGBD3
PGR
PHOX2A
PHOX2B
PITX1
PITX2
PITX3
PKNOX1
PKNOX2
PLAGL1
PLAGL2
PML
PO5F1_HUMAN
POU1F1
POU2AF1
POU2F1
POU2F3
POU3F1
POU3F2
POU3F3
POU3F4
POU4F1
POU4F3
POU5F1
POU6F1
PPARA
PPARD
PPARG
PPARGC1A
PPP1R13B
PPP1R13L
PREB
PROP1
PROX1
PRRX1
PTTG2
RARA
RARG
RAX
RB1
RBL1
RBL2
RBPJ
REL
RELA
RELB
RFX1
RFX2
RFX3
RFX5
RFXANK
RORA
RORB
RORC
RREB1
RUNX1
RUNX2
RUVBL1
RXRA
RXRB
RXRB_HUMAN
RXRG
SFPQ
SHOX
SHOX2
SIM1
SIM2
SIX1
SIX2
SIX3
SIX4
SIX6
SKI
SKIL
SLC12A8
SLC2A4RG
SMAD1
SMAD2
SMAD4
SMAD5
SMAD6
SMARCA2
SMARCA4
SMARCB1
SMARCC1
SNAI1
SNAI2
SNAPC1
SNAPC2
SNAPC3
SNW1
SOCS1
SOCS3
SOX1
SOX10
SOX11
SOX12
SOX14
SOX15
SOX17
SOX18
SOX2
SOX21
SOX3
SOX4
SOX5
SOX7
SOX8
SOX9
SP1
SP3
SP4
SPDEF
SPI1
SPIB
SREBF1
SREBF2
SRF
SRY
SS18
SS18L1
SSRP1
STAT1
STAT2
STAT3
STAT4
STAT5A
STAT5B
STAT6
STOX2
SUB1
SULT2A1
SUPT16H
T
TADA2L
TADA3L
TAF1
TAF10
TAF11
TAF12
TAF13
TAF1A
TAF1C
TAF4
TAF5
TAF6
TAF9
TAL1
TARBP2
TAZ
TBP
TBR1
TBX1
TBX18
TBX19
TBX2
TBX20
TBX21
TBX22
TBX3
TBX4
TBX5
TBX6
TCEB1
TCEB2
TCEB3
TCERG1
TCF12
TCF21
TCF3
TCF4
TCF7
TCF7L1
TEAD3
TEAD4
TEF
TFAM
TFAP2A
TFAP2C
TFAP4
TFCP2L1
TFDP1
TFEB
TGIF1
TGIF2
THRA
THRB
TLE1
TLX1
TLX2
TLX3
TOPORS
TP53
TP53BP1
TP63
TP73
TRIM24
TRIM33
TWIST1
UBP1
UBTF
USF1
USF2
VAV1
VAX2
VDR
VENTX
VEZF1
VPS72
VSX2
WT1
XBP1
XRCC5
XRCC6
YWHAE
YY1
ZBTB16
ZBTB17
ZBTB25
ZBTB33
ZBTB48
ZBTB6
ZBTB7A
ZEB1
ZEB2
ZFHX3
ZFP37
ZFX
ZFY
ZHX1
ZIC1
ZIC2
ZKSCAN5
ZNF10
ZNF12
ZNF146
ZNF174
ZNF187
ZNF20
ZNF219
ZNF238
ZNF24
ZNF281
ZNF33A
ZNF350
ZNF354A
ZNF398
ZNF423
ZNF43
ZNF44
ZNF45
ZNF628
ZNF7
ZNF76
ZNF83
ZNF85