MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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description	Rank	Gene	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 2030 to 2079 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

description	Rank	red	green	network_comparison
phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617]	1754	220.091	217.362	1.01256
pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059]	1250	219.354	224.7	1.02437
pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687]	993	211.071	204.205	1.03362
placenta growth factor precursor (plgf). [swissprot;acc:p49763]	3036	0.00001	0.00001	1
placental protein 11 precursor (ec 3.4.21.-) (pp11). [swissprot;acc:p21128]	3076
placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237]	796	224.244	234.511	1.04578
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872]	510	177.699	190.24	1.07057
plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120]	794	224.244	234.511	1.04578
platelet-activating factor acetylhydrolase ib alpha subunit (ec 3.1.1.47) (paf acetylhydrolase 45 kda subunit) (paf-ah 45 kda subunit) (paf-ah alpha) (pafah alpha) (lissencephaly-1 protein) (lis- 1). [swissprot;acc:p43034]	3221	0.00001	0.00001	1
pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832]	1259	219.354	224.7	1.02437
pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669]	522	222.893	208.523	1.06891
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	2094	207.321	205.747	1.00765
pnas-18. [sptrembl;acc:q9bzu3]	1463	161.056	164.211	1.01959
pogo transposable element with znf domain isoform 1. [refseq;acc:nm_015100]	2932	0.00001	0.00001	1
poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	1464	217.351	213.18	1.01957
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	984	116.71	120.654	1.03379
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	994	116.845	120.772	1.03361
polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940]	1700	217.624	214.69	1.01367
polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	1696
polyadenylate-binding protein 4 (poly(a)-binding protein 4) (pabp 4) (inducible poly(a)-binding protein) (ipabp) (activated-platelet protein-1) (app-1). [swissprot;acc:q13310]	1699
polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025]	1368	228.644	223.736	1.02194
polybromo 1. [refseq;acc:nm_018165]	2591	220.02	219.696	1.00147
polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710]	784	224.385	235.131	1.04789
polyhomeotic like 3; early development regulator 3; polyhomeotic 3. [refseq;acc:nm_024947]	2809	0.00001	0.00001	1
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195]	435	221.522	205.286	1.07909
polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999]	2095	229.266	227.53	1.00763
polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467]	429	239.709	259.038	1.08064
polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468]	451	239.092	257.705	1.07785
polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863]	1204	219.022	213.607	1.02535
polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780]	953	198.494	205.466	1.03512
polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481]	1811	216.854	214.35	1.01168
polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765]	1412	206.102	210.42	1.02095
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]	1414
polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190]	1382	218.47	213.876	1.02148
polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599]	1394		213.875
ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	918	212.952	205.292	1.03731
porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397]	2708	227.796	227.66	1.0006
possible global transcription activator snf2l1. [swissprot;acc:p28370]	2594	220.02	219.696	1.00147
possible global transcription activator snf2l2 (snf2-alpha). [swissprot;acc:p51531]	2596
possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532]	2593
postsynaptic protein cript; hspc139 protein. [refseq;acc:nm_014171]	3034	0.00001	0.00001	1
potassium channel modulatory factor 1; potassium channel modulatory factor; differentially expressed in branching tubulogenesis 91; zinc finger, zz domain containing 1. [refseq;acc:nm_020122]	2119	221.248	222.788	1.00696
potassium channel tetramerisation domain containing 3; ny-ren-45 antigen. [refseq;acc:nm_016121]	2975	0.00001	0.00001	1
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	145	265.639	319.546	1.20293
potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470]	475	226.727	210.816	1.07547
potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389]	474	226.789	210.818	1.07576
potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459]	476	226.681	210.814	1.07527
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	123	269.23	327.601	1.21681
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	120	269.278	327.709	1.21699
potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980]	122	269.248	327.642	1.21688

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.