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

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Showing element 451 to 500 of 12912 in total

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

Rank	description	red	network_comparison	green
451	n-myc proto-oncogene protein. [swissprot;acc:p04198]	4889.71	1.14745	5610.69
452	zinc finger-like protein 9. [refseq;acc:nm_033414]	3760.8	1.14738	4315.06
453	membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9]
454	guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915]
455	ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546]	4890.51	1.14731	5610.95
456	ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545]
457	nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217]
458	elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60]	4890.55		5610.96
459	myc proto-oncogene protein (c-myc). [swissprot;acc:p01106]	4892.16	1.14704	5611.48
460	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]	3790.11	1.14693	4346.98
461	grb2-related adaptor protein. [swissprot;acc:q13588]	5986.65	1.14683	6865.68
462	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858]	11383.2	1.14674	9926.61
463	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	3720.18	1.1463	4264.46
464	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	4858.96	1.1461	5568.85
465	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094]	3847.31	1.14605	4409.22
466	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
467	metastasis-associated protein mta1. [swissprot;acc:q13330]	4864.25	1.14583	5573.62
468	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028]	4869.15	1.14558	5578.02
469	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	3831.17	1.14554	4388.74
470	block of proliferation 1. [swissprot;acc:q14137]	3796.24	1.1455	4348.59
471	mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778]	9649.61	1.14549	11053.5
472	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1]
473	udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5]
474	rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1]
475	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137]
476	neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825]
477	nitrogen fixation cluster-like. [refseq;acc:nm_014301]
478	star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8]
479	star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502]
480	neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822]
481	mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635]
482	mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539]
483	neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681]
484	neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297]
485	sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0]
486	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975]	10908.6	1.14513	12491.8
487	pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328]	5277.4	1.14505	6042.88
488	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596]	10872.4	1.14483	12447
489	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	5281.11	1.14457	6044.61
490	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316]	15274.9	1.14445	13346.9
491	neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117]	5980.15	1.14437	6843.48
492	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443]	5979.94	1.14429	6842.76
493	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903]	5979.95		6842.78
494	e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140]	5979.93	1.14428	6842.72
495	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452]	10804.7		12363.6
496	nostrin. [refseq;acc:nm_052946]	4682.87	1.1441	4093.05
497	eap30 subunit of ell complex. [refseq;acc:nm_007241]
498	liv-1 protein, estrogen regulated. [refseq;acc:nm_012319]
499	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329]
500	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747]

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.