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. 2015 May 27;11(5):e1004939. doi: 10.1371/journal.ppat.1004939

Table 3. Transcription factors identified by iPOND and aniPOND.

Transcription Factors iPOND (Mutant) aniPOND (8hpi)
Experiment 1 Experiment 2 Experiment 1 Experiment 2
DNA-directed RNA polyermase II Ctrl 6hpi 8hpi 12hpi Ctrl 6hpi 8hpi 12hpi Ctrl Mutant KOS Ctrl Mutant KOS
POLR2A DNA-directed RNA polymerase II subunit RPB1 P24928 0 33 36 7 0 95 49 48 0 54 10 0 111 74
POLR2B DNA-directed RNA polymerase II subunit RPB2 P30876 0 20 40 4 0 97 61 51 0 31 3 0 87 50
POLR2C DNA-directed RNA polymerase II subunit RPB3 P19387 0 0 2 0 0 5 0 2 0 2 2 0 6 10
POLR2D DNA-directed RNA polymerase II subunit RPB4 O15514 0 0 2 0 0 2 0 0 2 0
POLR2E DNA-directed RNA polymerases II subunit RPB5 P19388 0 3 7 2 0 3 0 2 0 4 3 0 6 7
POLR2F DNA-directed RNA polymerases II subunit RPB6 P61218 0 2 0
POLR2G DNA-directed RNA polymerase II subunit RPB7 P62487 0 2 0 0 0 5 0 0 7 5
POLR2H DNA-directed RNA polymerases II subunit RPB8 P52434 0 2 2
POLR2I DNA-directed RNA polymerase II subunit RPB9 P36954 0 7 2
POLR2J DNA-directed RNA polymerase II subunit RPB11-a P52435 0 2 2 0
POLR2L DNA-directed RNA polymerases II subunit RPB10 P62875 0 2 0 0
Mediator of RNA polymerase II transcription
MED1 Mediator of RNA polymerase II transcription subunit 1 Q15648 0 6 8 0 52 32
MED4 Mediator of RNA polymerase II transcription subunit 4 Q9NPJ6 0 2 0 0 7 6
MED6 Mediator of RNA polymerase II transcription subunit 6 O75586 0 4 0 0 12 7
MED7 Mediator of RNA polymerase II transcription subunit 7 O43513 0 7 0
MED8 Mediator of RNA polymerase II transcription subunit 8 Q96G25 0 7 5
MED10 Mediator of RNA polymerase II transcription subunit 10 Q9BTT4 0 4 0
MED11 Mediator of RNA polymerase II transcription subunit 11 Q9P086 0 3 2
MED12 Mediator of RNA polymerase II transcription subunit 12 Q93074 0 14 0 0 82 46
MED13 Mediator of RNA polymerase II transcription subunit 13 Q9UHV7 0 6 0
MED13L Mediator of RNA polymerase II transcription subunit 13-like Q71F56 0 11 0
MED14 Mediator of RNA polymerase II transcription subunit 14 O60244 0 22 10 0 156 119
MED15 Mediator of RNA polymerase II transcription subunit 15 Q96RN5 0 15 3
MED16 Mediator of RNA polymerase II transcription subunit 16 Q9Y2X0 0 18 9 0 51 31
MED17 Mediator of RNA polymerase II transcription subunit 17 Q9NVC6 0 9 5 0 37 27
MED18 Mediator of RNA polymerase II transcription subunit 18 Q9BUE0 0 3 3 0 12 6
MED20 Mediator of RNA polymerase II transcription subunit 20 Q9H944 0 6 4 0 11 11
MED21 Mediator of RNA polymerase II transcription subunit 21 Q13503 0 2 0 0 4 2
MED22 Mediator of RNA polymerase II transcription subunit 22 Q15528 0 4 3
MED23 Mediator of RNA polymerase II transcription subunit 23 Q9ULK4 0 59 27 0 132 110
MED24 Mediator of RNA polymerase II transcription subunit 24 O75448 0 35 12 0 83 65
MED25 Mediator of RNA polymerase II transcription subunit 25 Q71SY5 0 16 16
MED27 Mediator of RNA polymerase II transcription subunit 27 Q6P2C8 0 4 2 0 16 17
MED28 Mediator of RNA polymerase II transcription subunit 28 Q9H204 0 2 2 0 3 4
MED29 Mediator of RNA polymerase II transcription subunit 29 Q9NX70 0 3 2 0 8 10
MED30 Mediator of RNA polymerase II transcription subunit 30 Q96HR3 0 4 0 0 7 4
MED31 Mediator of RNA polymerase II transcription subunit 31 Q9Y3C7 0 7 6 0 13 8
CCNC Cyclin-C P24863 0 2 3 0 6 5
CDK8 Cyclin-dependent kinase 8 P49336 0 8 10
Transcription initiation factor TFIID
TAF1 Transcription initiation factor TFIID subunit 1 P21675 0 5 12
TAF2 Transcription initiation factor TFIID subunit 2 Q6P1X5 0 9 0 0 18 25
TAF3 Transcription initiation factor TFIID subunit 3 Q5VWG9 0 0 3
TAF4 Transcription initiation factor TFIID subunit 4 O00268 0 5 0
TAF5 Transcription initiation factor TFIID subunit 5 Q15542 0 8 2 0 62 45
TAF6 Transcription initiation factor TFIID subunit 6 P49848 0 20 6 0 48 41
TAF9 Transcription initiation factor TFIID subunit 9 Q16594 0 8 10
TAF9B Transcription initiation factor TFIID subunit 9B Q9HBM6 0 8 3 0 6 0
TAF10 Transcription initiation factor TFIID subunit 10 Q12962 0 2 0 0 2 2
TAF12 Transcription initiation factor TFIID subunit 12 Q16514 0 4 0 0 2 3
TAF15 TATA-binding protein-associated factor 2N Q92804
TBP TATA-box binding protein P20226 0 12 17
Transcription initiation factor TFIIH
XPB TFIIH basal transcription factor complex helicase ERCC3 P19447 0 0 9 0 39 60
XPD TFIIH basal transcription factor complex helicase ERCC2 P18074 0 0 4 0 36 45
CDK7 Cyclin-dependent kinase 7 P50613 0 15 19
MAT1 CDK-activating kinase assembly factor MAT1 P51948 0 8 9
CCNH Cyclin-H P51946 0 0 2 0 8 9
GTF2H1 General transcription factor 2H subunit 1 P32780 0 6 14
GTF2H2 General transcription factor 2H subunit 2 Q6P1K8 0 2 6 0 21 38
GTF2H3 General transcription factor 2H subunit 3 Q13889 0 0 3 0 13 13
GTF2H4 General transcription factor 2H subunit 4 Q92759 0 0 5 0 17 36
Viral transcription regulators
VP16 Tegument protein VP16 P06492 4 11 16 85 21 6 52 108 9 86 81 13 127 158
ICP4 Major viral transcription factor P08392 46 300 199 247 31 259 266 366 133 613 585 113 1146 1255
ICP22 Transcriptional regulator ICP22 P04485 8 60 18 46 6 51 69 74 0 26 17 0 29 44
Other cellular transcription factors
TRIM28 Transcription intermediary factor 1-beta Q13263 0 130 94 117 3 81 121 162 0 26 19 0 121 181
CTCF Transcriptional repressor CTCF P49711 0 2 6 24 0 26 12 0 41 54
TFII-I General transcription factor II-I P78347 0 69 61 73 0 35 49 73 0 3 0 0 21 10
SPT5 Transcription elongation factor SUPT5H (DSIF component) O00267 0 25 7 6 0 33 20 27 0 15 2 0 37 21
SPT6 Transcription elongation factor SUPT6H Q7KZ85 0 5 6 0 0 28 10 14 0 17 0 0 38 14
CSK21 Casein kinase II subunit alpha P68400 0 7 3 0 9 12
CSK2B Casein kinase II subunit beta P67870 0 6 2 2 10 7
FUBP1 Far upstream element-binding protein 1 Q96AE4 2 25 32 47 7 32 31 39
FUBP2 Far upstream element-binding protein 2 Q92945 9 41 22 46 6 27 32 38
MATR3 Matrin-3 P43243 0 52 41 69 0 41 50 105 0 2 0 0 16 5
BCLF1 Bcl-2-associated transcription factor 1 Q9NYF8 0 0 14 15 0 12 13 29 10 23 14 16 54 47
CDC5L Cell division cycle 5-like protein Q99459 0 0 11 10 0 4 11 17 0 2 0 0 8 5
NONO Non-POU domain-containing octamer-binding protein Q15233 18 85 90 123 22 85 121 133 31 67 60 8 88 75
CN166 UPF0568 protein C14orf166 Q9Y224 0 9 5 10 0 2 3 14 0 2 6 0 7 16

Experiments, conditions, and complexes are indicated in bold. Columns 1, 2, and 3 include protein name, description, and accession number. Values indicate spectral counts determined by mass spectrometry.