1. Information
    majorVersion:3 minorVersion:0 projectID:local projectVersionID:undef fileName:/home/ikeda/eclipse/workspace/macrophage/csml/ok/csml/15183343.csml convertedTime:2009.07.01.10:46

  2. Original Literature
  3. Model OverView
  4. Model Abstracts
  5. Model Detail
  6. Download
Original Literature Model OverView
Publication
Title HIV-1 infection and regulation of Tat function in macrophages.
Authors Liou LY, Herrmann CH, Rice AP.
Affiliation Department of Molecular Virology and Microbiology, Baylor College of Medicine,One Baylor Plaza, Houston, TX 77030, USA.
Abstract The macrophage is an important cell type in the pathophysiology of humanimmunodeficiency virus type 1 (HIV-1) infection. Macrophages both support viralreplication and are capable of attracting and activating lymphocytes, thusrendering CD4+ T lymphocytes highly permissive for infection. The viral Tatprotein, whose function is mediated by the cellular cyclin T1 protein complexedwith CDK9, is required for efficient transcription of the integrated HIV-1provirus by RNA polymerase II. Cyclin T1 expression is highly regulated duringmacrophage differentiation, and this has important implications for HIV-1replication. In monocytes isolated from healthy blood donors, cyclin T1 proteinexpression is low and is induced to high levels within the first few days ofdifferentiation by a post-transcriptional mechanism. After 1-2 weeks ofmacrophage differentiation, however, cyclin T1 expression is shut off. Treatmentof macrophages with lipopolysaccharide (LPS) can re-induce cyclin T1, indicatingthat the activation status of macrophages can regulate cyclin T1 expression.Recent results indicate that HIV-1 infection is able to induce cyclin T1expression in macrophages. Future studies of cyclin T1 regulation in macrophagesmay suggest means of manipulating expression of this crucial cellular co-factorfor therapeutic benefit in HIV-1 infected individuals. Copyright 2004 ElsevierB.V.
PMID 15183343
Model Abstract

Entity

e1: e10: e11:DSIF:NELF:RNA polymerase II{p} e12:RNA:cyclinT1:Cdk9:Tat e13:Tat:cyclinT1:cdk9 e14:DSIF:NELF:RNA polymerase II e15:cyclinT1:cdk9 e16:Tat e17:NF-kappaB e18:7SK SnRNA e19:MAQ1 e2: e20:7SK SnRNA:Tat:cyclinT1:cdk9:MAQ1 e21:NF-kappaB{active} e22:PMA e23:7SK SnRNA:cyclinT1:Cdk9:Tat e24:Cyclin T1 e25:Cyclin T1 e26:protein remnants e27:proteasome inhibitors e28:LPS e3: e32:MIP1beta e33:MIP1alpha e34:MIP1alpha e35:MIP1beta e36:NEF e37:Cdk9 e38:cyclinT2a e39:Cdk9:cyclinT2a e4: e40:cyclin T2b e41:Cdk9:cyclinT2a e42:cyclin K e43:cyclinK:cdk9 e44:GM-CSF e45:GM-CSFR e46:GM-CSF:GMCSFR e47:IL4 e48:IL-4R e49:IL4:IL4R e5:Viral DNA e50: e51: e52: e53: e54: e55: e56: e57: e58: e59: e6:viral RNA e60: e61: e62: e7: e8: e9:

Process

p1 p10 p11 p12 p13 p15 p16 p17 p18 p19 p2 p20 p21 p22 p23 p3 p4 p5 p6 p7 p8 p9
Model Detail
227.75, 1.8768579754014318
910.061118527497, 1321.4087441019262

--

e1

cso30:c:EntityBiologicalCompartment

cso30:i:CC_PlasmaMembrane

--

--

--

true true true true

csml-variable:Double

m1

0

false

infinite

0

unit false true false

--

Go back
241.0, 100.0
829.9775981223105, 1167.545103664102

--

e10

cso30:c:EntityBiologicalCompartment

cso30:i:CC_Cytosol

--

--

--

true true true true

csml-variable:Double

m10

0

false

infinite

0

unit false true false

--

Go back
563.5, 616.2464672416958
33.50669847678473, 46.75353275830429

DSIF:NELF:RNA polymerase II{p}

--

e11

cso30:c:Complex

cso30:i:CC_Nucleoplasm

--

p3 p8

p5

true true true true

csml-variable:Double

m11

0

false

infinite

0

unit false false false

--

Go back
872.5, 805.8819966966416
38.06790236740687, 53.11800330335842

RNA:cyclinT1:Cdk9:Tat

--

e12

cso30:c:Complex

cso30:i:CC_Nucleoplasm

--

p2

p8

true true true true

csml-variable:Double

m12

0

false

infinite

0

unit false false false

--

Go back
744.5, 728.6247017801431
39.685630390897416, 55.37529821985686

Tat:cyclinT1:cdk9

--

e13

cso30:c:Complex

cso30:i:CC_Nucleoplasm

--

true true true true

csml-variable:Double

m13

0

false

infinite

0

unit false false false

--

Go back
563.5, 772.2464672416958
33.50669847678473, 46.75353275830429

DSIF:NELF:RNA polymerase II

--

e14

cso30:c:Complex

cso30:i:CC_Nucleoplasm

--

--

p1 p3 p8

true true true true

csml-variable:Double

m14

0

false

infinite

0

unit false false false

--

Go back
874.5, 650.7772037993667
35.298616897183805, 43.222796200633226

cyclinT1:cdk9

--

e15

cso30:c:Complex

cso30:i:CC_Nucleoplasm

--

--

p4

true true true true

csml-variable:Double

m15

0

false

infinite

0

unit false false false

--

Go back
849.5, 588.9585429663917
28.392231837391822, 46.041457033608374

Tat

--

e16

cso30:c:Protein

cso30:i:CC_Nucleoplasm

--

--

p4

true true true true

csml-variable:Double

m16

0

false

infinite

0

unit false false false

--

Go back
615.0, 372.51650231434894
50.243509760515195, 30.983497685651038

NF-kappaB

--

e17

cso30:c:Protein

cso30:i:CC_Cytosol

--

--

p9

true true true true

csml-variable:Double

m17

0

false

infinite

0

unit false false false

--

Go back
869.0, 735.7030878859857
37.6104513064133, 40.296912114014255

7SK SnRNA

--

e18

cso30:c:RnaOther

cso30:i:CC_Nucleoplasm

--

--

p6

true true true true

csml-variable:Double

m18

0

false

infinite

0

unit false false false

--

Go back
811.0, 530.7
34.4, 25.800000000000004

MAQ1

--

e19

cso30:c:Protein

cso30:i:CC_Nucleoplasm

--

--

p7

true true true true

csml-variable:Double

m19

0

false

infinite

0

unit false false false

--

Go back
227.75, 1.8768579754014318
910.061118527497, 1321.4087441019262

--

e2

cso30:c:EntityBiologicalCompartment

cso30:i:CC_PlasmaMembrane_ExternalSideOfPlasmaMembrane_

--

--

--

true true true true

csml-variable:Double

m2

0

false

infinite

0

unit false true false

--

Go back
758.5, 474.0
43.0, 60.0

7SK SnRNA:Tat:cyclinT1:cdk9:MAQ1

--

e20

cso30:c:Complex

cso30:i:CC_Cytosol

--

p7

p3 p8

true true true true

csml-variable:Double

m20

0

false

infinite

0

unit false false false

--

Go back
830.0, 372.2134232239887
52.356610988126384, 32.286576776011266

NF-kappaB{active}

--

e21

cso30:c:Protein

cso30:i:CC_Cytosol

--

true true true true

csml-variable:Double

m21

0

false

infinite

0

unit false false false

--

Go back
694.0, 183.0
60.0, 34.0

PMA

--

e22

cso30:c:SmallMolecule

cso30:i:CC_Cytosol

--

--

p9 p11

true true true true

csml-variable:Double

m22

0

false

infinite

0

unit false false false

--

Go back
696.5, 625.8819966966416
38.06790236740687, 53.11800330335842

7SK SnRNA:cyclinT1:Cdk9:Tat

--

e23

cso30:c:Complex

cso30:i:CC_Nucleoplasm

--

true true true true

csml-variable:Double

m23

0

false

infinite

0

unit false false false

--

Go back
386.0, 680.0
60.0, 32.0

Cyclin T1

--

e24

cso30:c:mRNA

cso30:i:CC_Nucleoplasm

--

--

p11 p13 p20 p23

true true true true

csml-variable:Double

m24

0

false

infinite

0

unit false false false

--

Go back
342.0, 395.5187160394445
51.86154155765748, 31.981283960555444

Cyclin T1

--

e25

cso30:c:Protein

cso30:i:CC_Cytosol

--

true true true true

csml-variable:Double

m25

0

false

infinite

0

unit false false false

--

Go back
452.0, 248.44342331993113
48.16197587593337, 46.556576680068936

protein remnants

--

e26

cso30:c:EntityBiological

cso30:i:CC_Cytosol

--

p12

--

true true true true

csml-variable:Double

m26

0

false

infinite

0

unit false false false

--

Go back
314.0, 185.81833473507146
51.497056349873844, 29.181665264928508

proteasome inhibitors

--

e27

cso30:c:SmallMolecule

cso30:i:CC_Cytosol

--

--

p12

true true true true

csml-variable:Double

m27

0

false

infinite

0

unit false false false

--

Go back
94.0, 727.0
60.0, 34.0

LPS

--

e28

cso30:c:SmallMolecule

cso30:i:CC_Extracellular

--

--

p13

true true true true

csml-variable:Double

m28

0

false

infinite

0

unit false false false

--

Go back
245.95122237054989, 20.078080345951417
873.6586737863964, 1285.0062993608271

--

e3

cso30:c:EntityBiologicalCompartment

cso30:i:CC_PlasmaMembrane_IntegralToPlasmaMembrane_

--

--

--

true true true true

csml-variable:Double

m3

0

false

infinite

0

unit false true false

--

Go back
1194.0, 605.5
60.0, 37.0

MIP1beta

--

e32

cso30:c:Protein

cso30:i:CC_Extracellular

--

p16

--

true true true true

csml-variable:Double

m32

0

false

infinite

0

unit false false false

--

Go back
1186.0, 797.5
60.0, 37.0

MIP1alpha

--

e33

cso30:c:Protein

cso30:i:CC_Extracellular

--

p15

--

true true true true

csml-variable:Double

m33

0

false

infinite

0

unit false false false

--

Go back
934.0, 796.0
60.0, 32.0

MIP1alpha

--

e34

cso30:c:mRNA

cso30:i:CC_Nucleoplasm

--

--

p15

true true true true

csml-variable:Double

m34

0

false

infinite

0

unit false false false

--

Go back
932.0, 717.0
55.32871972318339, 29.508650519031143

MIP1beta

--

e35

cso30:c:mRNA

cso30:i:CC_Nucleoplasm

--

--

p16

true true true true

csml-variable:Double

m35

0

false

infinite

0

unit false false false

--

Go back
951.0, 331.0486435921422
25.11225444340505, 57.95135640785781

NEF

--

e36

cso30:c:Protein

cso30:i:CC_Cytosol

--

--

p15 p16

true true true true

csml-variable:Double

m36

0

false

infinite

0

unit false false false

--

Go back
521.0, 498.36838398068016
45.618836788086135, 28.131616019319782

Cdk9

--

e37

cso30:c:Protein

cso30:i:CC_Cytosol

--

--

p17 p18 p19

true true true true

csml-variable:Double

m37

0

false

infinite

0

unit false false false

--

Go back
669.0, 467.18
45.76, 34.32

cyclinT2a

--

e38

cso30:c:Protein

cso30:i:CC_Nucleoplasm

--

--

p17

true true true true

csml-variable:Double

m38

0

false

infinite

0

unit false false false

--

Go back
597.5, 517.5475754040993
37.119480086652224, 45.45242459590069

Cdk9:cyclinT2a

--

e39

cso30:c:Complex

cso30:i:CC_Nucleoplasm

--

p17

--

true true true true

csml-variable:Double

m39

0

false

infinite

0

unit false false false

--

Go back
279.62348375606746, 51.93021949441369
806.3141510153622, 1221.3020210639029

--

e4

cso30:c:EntityBiologicalCompartment

cso30:i:CC_PlasmaMembrane_InternalSideOfPlasmaMembrane_

--

--

--

true true true true

csml-variable:Double

m4

0

false

infinite

0

unit false true false

--

Go back
436.0, 572.4999999999999
32.0, 24.0

cyclin T2b

--

e40

cso30:c:Protein

cso30:i:CC_Nucleoplasm

--

--

p18

true true true true

csml-variable:Double

m40

0

false

infinite

0

unit false false false

--

Go back
465.0, 654.6906077348067
30.878453038674028, 34.30939226519336

Cdk9:cyclinT2a

--

e41

cso30:c:Complex

cso30:i:CC_Extracellular

--

p18

--

true true true true

csml-variable:Double

m41

0

false

infinite

0

unit false false false

--

Go back
635.0, 584.3
41.599999999999994, 31.200000000000006

cyclin K

--

e42

cso30:c:Protein

cso30:i:CC_Extracellular

--

--

p19

true true true true

csml-variable:Double

m42

0

false

infinite

0

unit false false false

--

Go back
696.0, 530.0220994475139
39.58011049723757, 43.97790055248618

cyclinK:cdk9

--

e43

cso30:c:Complex

cso30:i:CC_Nucleoplasm

--

p19

--

true true true true

csml-variable:Double

m43

0

false

infinite

0

unit false false false

--

Go back
116.0, 340.78979673978665
48.17870798953513, 29.710203260213326

GM-CSF

--

e44

cso30:c:Protein

cso30:i:CC_Extracellular

--

--

p21

true true true true

csml-variable:Double

m44

0

false

infinite

0

unit false false false

--

Go back
240.5, 322.0
39.0, 60.0

GM-CSFR

--

e45

cso30:c:Protein

cso30:i:CC_PlasmaMembrane_IntegralToPlasmaMembrane_

--

--

p21

true true true true

csml-variable:Double

m45

0

false

infinite

0

unit false false false

--

Go back
244.5, 430.0
31.0, 60.0

GM-CSF:GMCSFR

--

e46

cso30:c:Complex

cso30:i:CC_PlasmaMembrane_IntegralToPlasmaMembrane_

--

true true true true

csml-variable:Double

m46

0

false

infinite

0

unit false false false

--

Go back
82.0, 527.9799999999999
43.36, 32.519999999999996

IL4

--

e47

cso30:c:Protein

cso30:i:CC_Extracellular

--

--

p22

true true true true

csml-variable:Double

m47

0

false

infinite

0

unit false false false

--

Go back
236.5, 538.0
39.0, 60.0

IL-4R

--

e48

cso30:c:Protein

cso30:i:CC_PlasmaMembrane_IntegralToPlasmaMembrane_

--

--

p22

true true true true

csml-variable:Double

m48

0

false

infinite

0

unit false false false

--

Go back
244.5, 654.0
31.0, 60.0

IL4:IL4R

--

e49

cso30:c:Complex

cso30:i:CC_PlasmaMembrane_IntegralToPlasmaMembrane_

--

true true true true

csml-variable:Double

m49

0

false

infinite

0

unit false false false

--

Go back
426.0, 877.5
60.0, 21.0

Viral DNA

--

e5

cso30:c:Dna

cso30:i:CC_Nucleoplasm

--

--

p1 p5 p10

true true true true

csml-variable:Double

m5

0

false

infinite

0

unit false false false

--

Go back
339.0, 442.6869341512892
682.1184823932803, 618.6065194143904

--

e50

cso30:c:EntityBiologicalCompartment

cso30:i:CC_NuclearEnvelopeLumen

--

--

--

true true true true

csml-variable:Double

m50

0

false

infinite

0

unit false true false

--

Go back
412.6738770555123, 457.34700934898603
398.8551275074305, 599.5529305207235

--

e51

cso30:c:EntityBiologicalCompartment

cso30:i:CC_NuclearPore

--

--

--

true true true true

csml-variable:Double

m51

0

false

infinite

0

unit false true false

--

Go back
347.8916748170445, 450.943489338545
664.3351327591913, 602.0934090398787

--

e52

cso30:c:EntityBiologicalCompartment

cso30:i:CC_NuclearInnerMembrane

--

--

--

true true true true

csml-variable:Double

m52

0

false

infinite

0

unit false true false

--

Go back
349.1619140766227, 452.21372859812243
661.7946542400356, 599.5529305207235

--

e53

cso30:c:EntityBiologicalCompartment

cso30:i:CC_NuclearLumen

--

--

--

true true true true

csml-variable:Double

m53

0

false

infinite

0

unit false true false

--

Go back
339.0, 442.6869341512892
682.1184823932803, 618.6065194143904

--

e54

cso30:c:EntityBiologicalCompartment

cso30:i:CC_NuclearOuterMembrane

--

--

--

true true true true

csml-variable:Double

m54

0

false

infinite

0

unit false true false

--

Go back
339.0, 442.6869341512892
682.1184823932803, 618.6065194143904

--

e55

cso30:c:EntityBiologicalCompartment

cso30:i:CC_Nucleus

--

--

--

true true true true

csml-variable:Double

m55

0

false

infinite

0

unit false true false

--

Go back
349.1619140766227, 452.21372859812243
661.7946542400356, 599.5529305207235

--

e56

cso30:c:EntityBiologicalCompartment

cso30:i:CC_Nucleoplasm

--

--

--

true true true true

csml-variable:Double

m56

0

false

infinite

0

unit false true false

--

Go back
836.9337897544988, 696.73478606685
42.61501487715179, 38.577802941421695

--

e57

cso30:c:EntityBiologicalCompartment

cso30:i:CC_NuclearBody

--

--

--

true true true true

csml-variable:Double

m57

0

false

infinite

0

unit false true false

--

Go back
725.1527349116521, 874.5682824077419
120.6727296598913, 109.24057632369123

--

e58

cso30:c:EntityBiologicalCompartment

cso30:i:CC_Nucleolus

--

--

--

true true true true

csml-variable:Double

m58

0

false

infinite

0

unit false true false

--

Go back
339.0, 442.6869341512892
682.1184823932803, 618.6065194143904

--

e59

cso30:c:EntityBiologicalCompartment

cso30:i:CC_NuclearEnvelope

--

--

--

true true true true

csml-variable:Double

m59

0

false

infinite

0

unit false true false

--

Go back
734.0, 872.5
60.0, 31.0

viral RNA

--

e6

cso30:c:Rna

cso30:i:CC_Nucleoplasm

--

true true true true

csml-variable:Double

m6

0

false

infinite

0

unit false false false

--

Go back
499.7714882835721, 717.5905597912939
21.601690069567393, 10.40081373719913

--

e60

cso30:c:EntityBiologicalCompartment

cso30:i:CC_Chromatin

--

--

--

true true true true

csml-variable:Double

m60

0

false

infinite

0

unit false true false

--

Go back
499.05014670680305, 686.5728719902278
73.93751161882115, 133.08752091387817

--

e61

cso30:c:EntityBiologicalCompartment

cso30:i:CC_NuclearChromosome

--

--

--

true true true true

csml-variable:Double

m61

0

false

infinite

0

unit false true false

--

Go back
530.0678345078702, 773.1338612025068
11.54146522830378, 11.54146522830379

--

e62

cso30:c:EntityBiologicalCompartment

cso30:i:CC_NuclearCentromere

--

--

--

true true true true

csml-variable:Double

m62

0

false

infinite

0

unit false true false

--

Go back
292.0, 57.0
839.7237354966342, 1189.8668429177399

--

e7

cso30:c:EntityBiologicalCompartment

cso30:i:CC_Cell

--

--

--

true true true true

csml-variable:Double

m7

0

false

infinite

0

unit false true false

--

Go back
242.0, 106.0
805.5569854171277, 1169.6687428256696

--

e8

cso30:c:EntityBiologicalCompartment

cso30:i:CC_Cell_WithoutCellWall_

--

--

--

true true true true

csml-variable:Double

m8

0

false

infinite

0

unit false true false

--

Go back
250.0, 127.0
801.8791759029863, 1154.3288303559784

--

e9

cso30:c:EntityBiologicalCompartment

cso30:i:CC_Cytoplasm

--

--

--

true true true true

csml-variable:Double

m9

0

false

infinite

0

unit false true false

--

Go back
566.0, 874.0
28.0, 28.0

p1

p1

cso30:i:ME_Transcription

cso30:i:CC_Nucleoplasm

--

true true true true

--

and

mass

coefficient1:0.1
coefficient2:1.0
stoichiometry:c1 : 1
stoichiometry:c3 : 1
stoichiometry:c2 : 1

m5*m14*0.1

nodelay

--

true

0

false

PMID: 15183343 In the absence of the viral Tat protein, RNA polymerase II initiates transcription from the viral LTR, but is defective for elongation and few productive transcripts are made. PMID: 15183343, 11713532, 11713533 A small nuclear RNA known as 7SK snRNA has been found to associate with a significant portion of P-TEFb and negatively regulate kinase activity in vitro, leading to the proposal that 7SK snRNA is a negative regulator of P-TEFb function.

Go back
643.0, 923.0
25.0, 25.0

p10

p10

cso30:i:ME_Transcription

cso30:i:CC_Nucleoplasm

--

true true true true

--

and

mass

coefficient1:0.1
coefficient2:1.0
stoichiometry:c29 : 1
stoichiometry:c31 : 1
stoichiometry:c30 : 1

m5*m21*0.1

nodelay

--

true

0

false

PMID: 15183343, 2654643 NF-¦ÊB is induced under viral infected conditions and contributes to an increase in LTR transcription and viral replication. PMID: 15183343, 11713532, 11713533 A small nuclear RNA known as 7SK snRNA has been found to associate with a significant portion of P-TEFb and negatively regulate kinase activity in vitro, leading to the proposal that 7SK snRNA is a negative regulator of P-TEFb function.

Go back
435.0, 459.0
25.0, 25.0

p11

p11

cso30:i:ME_Translation

cso30:i:CC_Cytosol

--

true true true true

--

and

mass

coefficient1:0.1
coefficient2:1.0
stoichiometry:c33 : 1
stoichiometry:c35 : 1
stoichiometry:c34 : 1

m24*m22*0.1

nodelay

--

true

0

false

PMID: 15183343 PMA treatment of U937 and HL-60 cells produced an increase of cyclin T1 protein expression from very low levels

Go back
395.0, 343.0
26.0, 26.0

p12

p12

cso30:i:ME_ProteasomeDegradation

cso30:i:CC_Cytosol

--

true true true true

--

and

mass

coefficient1:0.1
coefficient2:1.0
stoichiometry:c36 : 1
stoichiometry:c38 : 1
stoichiometry:c37 : 1

m25*0.1

nodelay

--

true

0

false

PMID: 15183343, 15254183 Using proteasome inhibitors, we have recently observed that the shut off of cyclin T1 in uninfected late-differentiated macrophages involves proteasome-mediated proteolysis.

Go back
383.0, 483.0
25.0, 25.0

p13

p13

cso30:i:ME_Translation

cso30:i:CC_Cytosol

--

true true true true

--

and

mass

coefficient1:0.1
coefficient2:1.0
stoichiometry:c39 : 1
stoichiometry:c40 : 1
stoichiometry:c41 : 1

m24*m28*0.1

nodelay

--

true

0

false

PMID: 15183343, 12368300 We observed that treatment of macrophages with lipopolysaccharide (LPS) at late time points of differentiation re-induces cyclin T1 protein expression.

Go back
1034.0, 806.0
19.0, 19.0

p15

p15

cso30:i:ME_Translation

cso30:i:CC_Cytosol

--

true true true true

--

and

mass

coefficient1:0.1
coefficient2:1.0
stoichiometry:c44 : 1
stoichiometry:c49 : 1
stoichiometry:c45 : 1

m34*m36*0.1

nodelay

--

true

0

false

PMID: 15183343 HIV-infected macrophages secrete at least two chemokines, MIP1¦Á and MIP1¦Â, which recruit and activate resting CD4+ T lymphocytes.Analysis of viral genes involved in the secretion of these chemokines revealed that the HIV-1 Nef protein is responsible for the induction of chemokines.

Go back
1036.0, 612.0
23.0, 23.0

p16

p16

cso30:i:ME_Translation

cso30:i:CC_Cytosol

--

true true true true

--

and

mass

coefficient1:0.1
coefficient2:1.0
stoichiometry:c46 : 1
stoichiometry:c48 : 1
stoichiometry:c47 : 1

m35*m36*0.1

nodelay

--

true

0

false

PMID: 15183343 HIV-infected macrophages secrete at least two chemokines, MIP1¦Á and MIP1¦Â, which recruit and activate resting CD4+ T lymphocytes.Analysis of viral genes involved in the secretion of these chemokines revealed that the HIV-1 Nef protein is responsible for the induction of chemokines.

Go back
601.0, 473.0
21.0, 21.0

p17

p17

cso30:i:ME_Binding

cso30:i:CC_Nucleoplasm

--

true true true true

--

and

mass

coefficient1:0.1
coefficient2:1.0
stoichiometry:c50 : 1
stoichiometry:c51 : 1
stoichiometry:c52 : 1

m37*m38*0.1

nodelay

--

true

0

false

PMID: 15183343 CDK9 is also found in other complexes that contain regulatory subunits other than cyclin T1; these additional cyclin partners of CDK9 are cyclins T2a, T2b, and K.

Go back
472.0, 528.0
23.0, 23.0

p18

p18

cso30:i:ME_Binding

cso30:i:CC_Nucleoplasm

--

true true true true

--

and

mass

coefficient1:0.1
coefficient2:1.0
stoichiometry:c53 : 1
stoichiometry:c54 : 1
stoichiometry:c55 : 1

m40*m37*0.1

nodelay

--

true

0

false

PMID: 15183343 CDK9 is also found in other complexes that contain regulatory subunits other than cyclin T1; these additional cyclin partners of CDK9 are cyclins T2a, T2b, and K.

Go back
532.0, 568.0
23.0, 23.0

p19

p19

cso30:i:ME_Binding

cso30:i:CC_Extracellular

--

true true true true

--

and

mass

coefficient1:0.1
coefficient2:1.0
stoichiometry:c56 : 1
stoichiometry:c57 : 1
stoichiometry:c58 : 1

m37*m42*0.1

nodelay

--

true

0

false

PMID: 15183343 CDK9 is also found in other complexes that contain regulatory subunits other than cyclin T1; these additional cyclin partners of CDK9 are cyclins T2a, T2b, and K.

Go back
754.0, 822.0
19.0, 19.0

p2

p2

cso30:i:ME_Binding

cso30:i:CC_Nucleoplasm

--

true true true true

--

and

mass

coefficient1:0.1
coefficient2:1.0
stoichiometry:c5 : 1
stoichiometry:c4 : 1
stoichiometry:c6 : 1

m6*m13*0.1

nodelay

--

true

0

false

PMID: 15183343 Tat binds to TAR RNA in a complex with a cellular protein kinase complex termed TAK/P-TEFb (Tat-associated kinase/positive transcriptional elongation factor b). TAK/P-TEFb is composed of cyclin T1 as a regulatory subunit and CDK9 as the catalytic subunit.

Go back
354.0, 546.0
27.0, 27.0

p20

p20

cso30:i:ME_Translation

cso30:i:CC_Cytosol

--

true true true true

--

and

mass

coefficient1:0.1
coefficient2:1.0
stoichiometry:c59 : 1
stoichiometry:c64 : 1
stoichiometry:c60 : 1

m24*m46*0.1

nodelay

--

true

0

false

PMID: 15183343, 12368300 The transient increase of cyclin T1 expression is specific to macrophage differentiation, as monocytes induced to differentiate to dendritic cells by GM-CSF and IL-4 sustain cyclin T1 expression.

Go back
183.0, 393.5
22.5, 22.5

p21

p21

cso30:i:ME_Binding

cso30:i:CC_Extracellular

--

true true true true

--

and

mass

coefficient1:0.1
coefficient2:1.0
stoichiometry:c61 : 1
stoichiometry:c62 : 1
stoichiometry:c63 : 1

m45*m44*0.1

nodelay

--

true

0

false

PMID: 15183343, 12368300 The transient increase of cyclin T1 expression is specific to macrophage differentiation, as monocytes induced to differentiate to dendritic cells by GM-CSF and IL-4 sustain cyclin T1 expression.

Go back
163.0, 567.0
25.0, 25.0

p22

p22

cso30:i:ME_Binding

cso30:i:CC_Extracellular

--

true true true true

--

and

mass

coefficient1:0.1
coefficient2:1.0
stoichiometry:c65 : 1
stoichiometry:c66 : 1
stoichiometry:c67 : 1

m47*m48*0.1

nodelay

--

true

0

false

PMID: 15183343, 12368300 The transient increase of cyclin T1 expression is specific to macrophage differentiation, as monocytes induced to differentiate to dendritic cells by GM-CSF and IL-4 sustain cyclin T1 expression.

Go back
306.0, 582.0
27.0, 27.0

p23

p23

cso30:i:ME_Translation

cso30:i:CC_Cytosol

--

true true true true

--

and

mass

coefficient1:0.1
coefficient2:1.0
stoichiometry:c68 : 1
stoichiometry:c70 : 1
stoichiometry:c69 : 1

m24*m49*0.1

nodelay

--

true

0

false

PMID: 15183343, 12368300 The transient increase of cyclin T1 expression is specific to macrophage differentiation, as monocytes induced to differentiate to dendritic cells by GM-CSF and IL-4 sustain cyclin T1 expression.

Go back
568.0, 708.5
23.5, 23.5

p3

p3

cso30:i:ME_Phosphorylation

cso30:i:CC_Nucleoplasm

--

true true true true

--

and

mass

coefficient1:0.1
coefficient2:1.0
stoichiometry:c7 : 1
stoichiometry:c19 : 1
stoichiometry:c24 : 1
stoichiometry:c20 : 1
stoichiometry:c8 : 1

m14*m13*0.1

nodelay

--

true

0

false

PMID: 15183343, 11145967, 10757782, 11713532, 11713533 Binding of Tat complexed with TAK/P-TEFb to TAR RNA is believed to activate transcriptional elongation through the phosphorylation of the carboxyl terminal domain of RNA polymerase II, the Spt5 subunit of a negative factor termed DSIF, and perhaps other substrates in the polymerase complex. A small nuclear RNA known as 7SK snRNA has been found to associate with a significant portion of P-TEFb and negatively regulate kinase activity in vitro, leading to the proposal that 7SK snRNA is a negative regulator of P-TEFb function. PMID: 15183343 Association of TAK/P-TEFb with 7SK snRNA and MAQ1 reduces CDK9 kinase activity in vitro.

Go back
805.0, 661.0
21.0, 21.0

p4

p4

cso30:i:ME_Binding

cso30:i:CC_Nucleoplasm

--

true true true true

--

and

mass

coefficient1:0.1
coefficient2:1.0
stoichiometry:c10 : 1
stoichiometry:c11 : 1
stoichiometry:c12 : 1

m16*m15*0.1

nodelay

--

true

0

false

PMID: 15183343 Tat makes direct protein-protein complex with cyclin T1 and can therefore only target the cyclin T1-containing P-TEFb complex. PMID: 15183343 TAK/P-TEFb is composed of cyclin T1 as a regulatory subunit and CDK9 as the catalytic subunit.

Go back
658.0, 818.0
27.0, 27.0

p5

p5

cso30:i:ME_Transcription

cso30:i:CC_Nucleoplasm

--

true true true true

--

and

mass

coefficient1:0.1
coefficient2:1.0
stoichiometry:c13 : 1
stoichiometry:c15 : 1
stoichiometry:c14 : 1

m5*m11*0.1

nodelay

--

true

0

false

PMID: 15183343 phosphorylation overcomes the active of negative factors (DSIF, NELF) that repress elongation

Go back
822.0, 746.0
19.0, 19.0

p6

p6

cso30:i:ME_Binding

cso30:i:CC_Nucleoplasm

--

true true true true

--

and

mass

coefficient1:0.1
coefficient2:1.0
stoichiometry:c16 : 1
stoichiometry:c17 : 1
stoichiometry:c18 : 1

m13*m18*0.1

nodelay

--

true

0

false

PMID: 15183343, 11713532, 11713533 A small nuclear RNA known as 7SK snRNA has been found to associate with a significant portion of P-TEFb and negatively regulate kinase activity in vitro, leading to the proposal that 7SK snRNA is a negative regulator of P-TEFb function.

Go back
787.0, 587.0
25.0, 25.0

p7

p7

cso30:i:ME_Binding

cso30:i:CC_Nucleoplasm

--

true true true true

--

and

mass

coefficient1:0.1
coefficient2:1.0
stoichiometry:c21 : 1
stoichiometry:c9 : 1
stoichiometry:c22 : 1

m19*m23*0.1

nodelay

--

true

0

false

PMID: 15183343, 12832472 A recent study has identified an additional protein termed MAQ1 that is associated with the 7SK/P-TEFb complex, and this association is dependent upon active RNA polymerase II transcription.

Go back
636.0, 700.5
23.5, 23.5

p3

p8

cso30:i:ME_Phosphorylation

cso30:i:CC_Nucleoplasm

--

true true true true

--

and

mass

coefficient1:0.1
coefficient2:1.0
stoichiometry:c23 : 1
stoichiometry:c25 : 1
stoichiometry:c42 : 1
stoichiometry:c43 : 1
stoichiometry:c26 : 1

m12*m14*0.1

nodelay

--

true

0

false

PMID: 15183343, 11145967, 10757782, 11713532, 11713533 Binding of Tat complexed with TAK/P-TEFb to TAR RNA is believed to activate transcriptional elongation through the phosphorylation of the carboxyl terminal domain of RNA polymerase II, the Spt5 subunit of a negative factor termed DSIF, and perhaps other substrates in the polymerase complex. A small nuclear RNA known as 7SK snRNA has been found to associate with a significant portion of P-TEFb and negatively regulate kinase activity in vitro, leading to the proposal that 7SK snRNA is a negative regulator of P-TEFb function. PMID: 15183343 Association of TAK/P-TEFb with 7SK snRNA and MAQ1 reduces CDK9 kinase activity in vitro.

Go back
711.0, 375.0
25.0, 25.0

p9

p9

cso30:i:ME_UnknownActivation

cso30:i:CC_Cytosol

--

true true true true

--

and

mass

coefficient1:0.1
coefficient2:1.0
stoichiometry:c27 : 1
stoichiometry:c32 : 1
stoichiometry:c28 : 1

m17*m22*0.1

nodelay

--

true

0

false

PMID: 15183343, 2654643 NF-¦ÊB is induced under viral infected conditions and contributes to an increase in LTR transcription and viral replication.

Go back
486.0, 888.0

c1

c1

cso30:c:InputAssociation

--

true true true true

cso30:c:InputAssociation

threshold

--

0

1,

--

Go back
830.0220196095182, 630.0

c10

c10

cso30:c:InputProcess

--

true true true true

cso30:c:InputProcess

threshold

--

0

1,

--

Go back
834.0, 672.0

c11

c11

cso30:c:InputProcess

--

true true true true

cso30:c:InputProcess

threshold

--

0

1,

--

Go back
785.2008586163729, 682.0

c12

c12

cso30:c:OutputProcess

--

true true true true

cso30:c:OutputProcess

threshold

--

0

1,

--

Go back
486.0, 837.9826659998611

c13

c13

cso30:c:InputAssociation

--

true true true true

cso30:c:InputAssociation

threshold

--

0

1,

--

Go back
685.0, 840.0

c14

c14

cso30:c:OutputProcess

--

true true true true

cso30:c:OutputProcess

threshold

--

0

1,

--

Go back
591.0, 663.0

c15

c15

cso30:c:InputAssociation

--

true true true true

cso30:c:InputAssociation

threshold

--

0

1,

--

Go back
784.0, 756.0

c16

c16

cso30:c:InputProcess

--

true true true true

cso30:c:InputProcess

threshold

--

0

1,

--

Go back
849.0, 756.0

c17

c17

cso30:c:InputProcess

--

true true true true

cso30:c:InputProcess

threshold

--

0

1,

--

Go back
740.9565555251719, 674.3403601260162

c18

c18

cso30:c:OutputProcess

--

true true true true

cso30:c:OutputProcess

threshold

--

0

1,

--

Go back
595.5845103431535, 662.0

c19

c19

cso30:c:InputInhibitor

--

true true true true

cso30:c:InputInhibitor

threshold

--

0

1,

--

Go back
594.0, 888.0

c2

c2

cso30:c:OutputProcess

--

true true true true

cso30:c:OutputProcess

threshold

--

0

1,

--

Go back
593.7131204109322, 527.0

c20

c20

cso30:c:InputInhibitor

--

true true true true

cso30:c:InputInhibitor

threshold

--

0

1,

--

Go back
810.5777087639997, 557.0

c21

c21

cso30:c:InputProcess

--

true true true true

cso30:c:InputProcess

threshold

--

0

1,

--

Go back
787.6257316546618, 541.833070699734

c22

c22

cso30:c:OutputProcess

--

true true true true

cso30:c:OutputProcess

threshold

--

0

1,

--

Go back
667.1888496020608, 721.5100486319922

c23

c23

cso30:c:InputAssociation

--

true true true true

cso30:c:InputAssociation

threshold

--

0

1,

--

Go back
599.8505099974172, 723.5393156857681

c24

c24

cso30:c:InputAssociation

--

true true true true

cso30:c:InputAssociation

threshold

--

0

1,

--

Go back
597.0, 730.2350053664503

c25

c25

cso30:c:InputProcess

--

true true true true

cso30:c:InputProcess

threshold

--

0

1,

--

Go back
602.4488315398183, 663.8574939053046

c26

c26

cso30:c:OutputProcess

--

true true true true

cso30:c:OutputProcess

threshold

--

0

1,

--

Go back
665.0, 388.0

c27

c27

cso30:c:InputProcess

--

true true true true

cso30:c:InputProcess

threshold

--

0

1,

--

Go back
736.0, 388.0

c28

c28

cso30:c:OutputProcess

--

true true true true

cso30:c:OutputProcess

threshold

--

0

1,

--

Go back
486.0, 895.0

c29

c29

cso30:c:InputAssociation

--

true true true true

cso30:c:InputAssociation

threshold

--

0

1,

--

Go back
580.0, 819.0

c3

c3

cso30:c:InputAssociation

--

true true true true

cso30:c:InputAssociation

threshold

--

0

1,

--

Go back
668.0, 904.3104235544095

c30

c30

cso30:c:OutputProcess

--

true true true true

cso30:c:OutputProcess

threshold

--

0

1,

--

Go back
663.7374330022586, 404.0

c31

c31

cso30:c:InputAssociation

--

true true true true

cso30:c:InputAssociation

threshold

--

0

1,

--

Go back
724.0, 217.0

c32

c32

cso30:c:InputAssociation

--

true true true true

cso30:c:InputAssociation

threshold

--

0

1,

--

Go back
418.0, 491.9195959492893

c33

c33

cso30:c:InputAssociation

--

true true true true

cso30:c:InputAssociation

threshold

--

0

1,

--

Go back
395.36662955296686, 431.8441746598661

c34

c34

cso30:c:OutputProcess

--

true true true true

cso30:c:OutputProcess

threshold

--

0

1,

--

Go back
465.7028426391131, 217.0

c35

c35

cso30:c:InputAssociation

--

true true true true

cso30:c:InputAssociation

threshold

--

0

1,

--

Go back
380.0, 375.5424513544061

c36

c36

cso30:c:InputProcess

--

true true true true

cso30:c:InputProcess

threshold

--

0

1,

--

Go back
418.0, 301.2089120009301

c37

c37

cso30:c:OutputProcess

--

true true true true

cso30:c:OutputProcess

threshold

--

0

1,

--

Go back
347.0, 215.0

c38

c38

cso30:c:InputInhibitor

--

true true true true

cso30:c:InputInhibitor

threshold

--

0

1,

--

Go back
397.7868636606043, 515.9612088014082

c39

c39

cso30:c:InputAssociation

--

true true true true

cso30:c:InputAssociation

threshold

--

0

1,

--

Go back
764.0, 784.0

c4

c4

cso30:c:InputProcess

--

true true true true

cso30:c:InputProcess

threshold

--

0

1,

--

Go back
143.0, 513.3924031531135

c40

c40

cso30:c:InputAssociation

--

true true true true

cso30:c:InputAssociation

threshold

--

0

1,

--

Go back
375.5703707579981, 434.5758296025207

c41

c41

cso30:c:OutputProcess

--

true true true true

cso30:c:OutputProcess

threshold

--

0

1,

--

Go back
657.143574990062, 534.0

c42

c42

cso30:c:InputInhibitor

--

true true true true

cso30:c:InputInhibitor

threshold

--

0

1,

--

Go back
662.9851817378741, 669.0

c43

c43

cso30:c:InputInhibitor

--

true true true true

cso30:c:InputInhibitor

threshold

--

0

1,

--

Go back
994.0, 814.0

c44

c44

cso30:c:InputAssociation

--

true true true true

cso30:c:InputAssociation

threshold

--

0

1,

--

Go back
1053.0, 816.0

c45

c45

cso30:c:OutputProcess

--

true true true true

cso30:c:OutputProcess

threshold

--

0

1,

--

Go back
972.0, 641.1950230741415

c46

c46

cso30:c:InputAssociation

--

true true true true

cso30:c:InputAssociation

threshold

--

0

1,

--

Go back
1059.0, 624.0

c47

c47

cso30:c:OutputProcess

--

true true true true

cso30:c:OutputProcess

threshold

--

0

1,

--

Go back
973.0, 389.0

c48

c48

cso30:c:InputAssociation

--

true true true true

cso30:c:InputAssociation

threshold

--

0

1,

--

Go back
969.0, 389.0

c49

c49

cso30:c:InputAssociation

--

true true true true

cso30:c:InputAssociation

threshold

--

0

1,

--

Go back
764.0, 849.0

c5

c5

cso30:c:InputProcess

--

true true true true

cso30:c:InputProcess

threshold

--

0

1,

--

Go back
567.0, 491.0459984420344

c50

c50

cso30:c:InputProcess

--

true true true true

cso30:c:InputProcess

threshold

--

0

1,

--

Go back
630.0, 484.0

c51

c51

cso30:c:InputProcess

--

true true true true

cso30:c:InputProcess

threshold

--

0

1,

--

Go back
613.0, 494.0

c52

c52

cso30:c:OutputProcess

--

true true true true

cso30:c:OutputProcess

threshold

--

0

1,

--

Go back
460.0, 557.36345376026

c53

c53

cso30:c:InputProcess

--

true true true true

cso30:c:InputProcess

threshold

--

0

1,

--

Go back
502.2636750760036, 523.0

c54

c54

cso30:c:InputProcess

--

true true true true

cso30:c:InputProcess

threshold

--

0

1,

--

Go back
481.2306732790395, 551.0

c55

c55

cso30:c:OutputProcess

--

true true true true

cso30:c:OutputProcess

threshold

--

0

1,

--

Go back
544.0, 527.0

c56

c56

cso30:c:InputProcess

--

true true true true

cso30:c:InputProcess

threshold

--

0

1,

--

Go back
562.8802437372457, 583.379042654018

c57

c57

cso30:c:InputProcess

--

true true true true

cso30:c:InputProcess

threshold

--

0

1,

--

Go back
555.0, 556.287942043912

c58

c58

cso30:c:OutputProcess

--

true true true true

cso30:c:OutputProcess

threshold

--

0

1,

--

Go back
375.6144574458186, 580.5607282892591

c59

c59

cso30:c:InputAssociation

--

true true true true

cso30:c:InputAssociation

threshold

--

0

1,

--

Go back
773.0, 832.0

c6

c6

cso30:c:OutputProcess

--

true true true true

cso30:c:OutputProcess

threshold

--

0

1,

--

Go back
368.0, 435.0

c60

c60

cso30:c:OutputProcess

--

true true true true

cso30:c:OutputProcess

threshold

--

0

1,

--

Go back
212.24695047554425, 368.0

c61

c61

cso30:c:InputProcess

--

true true true true

cso30:c:InputProcess

threshold

--

0

1,

--

Go back
156.0, 371.0

c62

c62

cso30:c:InputProcess

--

true true true true

cso30:c:InputProcess

threshold

--

0

1,

--

Go back
206.0, 414.0

c63

c63

cso30:c:OutputProcess

--

true true true true

cso30:c:OutputProcess

threshold

--

0

1,

--

Go back
276.0, 474.0

c64

c64

cso30:c:InputAssociation

--

true true true true

cso30:c:InputAssociation

threshold

--

0

1,

--

Go back
125.0, 554.0

c65

c65

cso30:c:InputProcess

--

true true true true

cso30:c:InputProcess

threshold

--

0

1,

--

Go back
195.91959594928935, 571.0

c66

c66

cso30:c:InputProcess

--

true true true true

cso30:c:InputProcess

threshold

--

0

1,

--

Go back
186.0, 592.0

c67

c67

cso30:c:OutputProcess

--

true true true true

cso30:c:OutputProcess

threshold

--

0

1,

--

Go back
338.533475233836, 614.7775991412111

c68

c68

cso30:c:InputAssociation

--

true true true true

cso30:c:InputAssociation

threshold

--

0

1,

--

Go back
324.0, 434.74621858967487

c69

c69

cso30:c:OutputProcess

--

true true true true

cso30:c:OutputProcess

threshold

--

0

1,

--

Go back
580.0, 740.0

c7

c7

cso30:c:InputProcess

--

true true true true

cso30:c:InputProcess

threshold

--

0

1,

--

Go back
276.0, 615.6367019809553

c70

c70

cso30:c:InputAssociation

--

true true true true

cso30:c:InputAssociation

threshold

--

0

1,

--

Go back
580.0, 671.0

c8

c8

cso30:c:OutputProcess

--

true true true true

cso30:c:OutputProcess

threshold

--

0

1,

--

Go back
735.0, 612.1927794053147

c9

c9

cso30:c:InputProcess

--

true true true true

cso30:c:InputProcess

threshold

--

0

1,

--

Go back