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

Results: HTML CSV LaTeX

Showing element 901 to 950 of 3730 in total

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

Rank	description	Filtered	red	green	network_comparison
451	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	0	2683.61	2642.79	1.01545
	n-myc proto-oncogene protein. [swissprot;acc:p04198]	1	4889.71	5610.69	1.14745
452	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]	0	1527.36	1504.85	1.01496
	zinc finger-like protein 9. [refseq;acc:nm_033414]	1	3760.8	4315.06	1.14738
453	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132]	0	1337.29	1356.52	1.01438
	membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9]	1	3760.8	4315.06	1.14738
454	guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915]
	transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724]	0	3219.3	3174.79	1.01402
455	ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546]	1	4890.51	5610.95	1.14731
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	0	2403.53	2371.24	1.01362
456	cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098]		17356	17126	1.01343
	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]	1	4890.51	5610.95	1.14731
457	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	0	1562.36	1541.69	1.01341
	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]	1	4890.51	5610.95	1.14731
458	elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60]		4890.55	5610.96
	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	0	2633.61	2668.56	1.01327
459	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]		3774.08	3821.87	1.01266
	myc proto-oncogene protein (c-myc). [swissprot;acc:p01106]	1	4892.16	5611.48	1.14704
460	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]	0	3693.07	3739.55	1.01259
	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]	1	3790.11	4346.98	1.14693
461	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	0	1915.69	1892.44	1.01229
	grb2-related adaptor protein. [swissprot;acc:q13588]	1	5986.65	6865.68	1.14683
462	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	0	11170.7	11305	1.01202
	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]	1	11383.2	9926.61	1.14674
463	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]		3720.18	4264.46	1.1463
	dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]	0	1262.65	1248.14	1.01163
464	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	1	4858.96	5568.85	1.1461
	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	0	2290.09	2264.37	1.01136
465	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]		6323	6254.09	1.01102
	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]	1	3847.31	4409.22	1.14605
466	ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]	0	1467.74	1483.62	1.01082
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	1	3847.31	4409.22	1.14605
467	metastasis-associated protein mta1. [swissprot;acc:q13330]		4864.25	5573.62	1.14583
	similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4]	0	2806.38	2782.56	1.00856
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]	1	4869.15	5578.02	1.14558
	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514]	0	599.896	604.911	1.00836
469	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	1	3831.17	4388.74	1.14554
	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	0	219.759	221.565	1.00822
470	block of proliferation 1. [swissprot;acc:q14137]	1	3796.24	4348.59	1.1455
	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	0	39165	39485	1.00817
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]	1	9649.61	11053.5	1.14549
	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	0	3855.78	3825.73	1.00785
472	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]		3889.5	3919.25	1.00765
	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1]	1	9649.61	11053.5	1.14549
473	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]	0	3889.5	3919.25	1.00765
	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]	1	9649.61	11053.5	1.14549
474	26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	0	2281.12	2263.85	1.00763
	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]	1	9649.61	11053.5	1.14549
475	alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652]	0	2319.24	2335.98	1.00722
	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137]	1	9649.61	11053.5	1.14549

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.