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

Results: HTML CSV LaTeX

Showing element 458 to 507 of 3228 in total

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

Rank	red	description	green	network_comparison
458	4890.55	elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60]	5610.96	1.14731
459	4892.16	myc proto-oncogene protein (c-myc). [swissprot;acc:p01106]	5611.48	1.14704
460	3790.11	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]	4346.98	1.14693
461	5986.65	grb2-related adaptor protein. [swissprot;acc:q13588]	6865.68	1.14683
462	11383.2	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]	9926.61	1.14674
463	3720.18	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	4264.46	1.1463
464	4858.96	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	5568.85	1.1461
465	3847.31	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]	4409.22	1.14605
466		transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
467	4864.25	metastasis-associated protein mta1. [swissprot;acc:q13330]	5573.62	1.14583
468	4869.15	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]	5578.02	1.14558
469	3831.17	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	4388.74	1.14554
470	3796.24	block of proliferation 1. [swissprot;acc:q14137]	4348.59	1.1455
471	9649.61	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]	11053.5	1.14549
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	10908.6	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975]	12491.8	1.14513
487	5277.4	pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328]	6042.88	1.14505
488	10872.4	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596]	12447	1.14483
489	5281.11	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	6044.61	1.14457
490	15274.9	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316]	13346.9	1.14445
491	5980.15	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]	6843.48	1.14437
492	5979.94	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443]	6842.76	1.14429
493	5979.95	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903]	6842.78
494	5979.93	e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140]	6842.72	1.14428
495	10804.7	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452]	12363.6
496	4682.87	nostrin. [refseq;acc:nm_052946]	4093.05	1.1441
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]
501		glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259]
502	6913.6	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	7907.05	1.1437
503	15182.5	tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625]	13277.9	1.14344
504	10067.9	enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084]	11511	1.14334
505	6856.71	signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191]	7838.3	1.14316
506	3893.85	eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537]	4450.98	1.14308
507	6875.08	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681]	7858.38	1.14302

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.