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	Interaction Map	Filtered	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 5008 to 5057 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
2504	ubiquitin-activating enzyme e1 (a1s9 protein). [swissprot;acc:p22314]	Subtracted	194.527	195.08	0.553
2505	calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [swissprot;acc:o75746]
	chromobox protein homolog 5 (heterochromatin protein 1 homolog alpha) (hp1 alpha) (antigen p25). [swissprot;acc:p45973]	Divided	187.853	188.326	1.00252
2506	44050 protein. [refseq;acc:nm_178832]		151.386	151.009	1.0025
	melanoma antigen recognized by t cells 2. [refseq;acc:nm_018194]	Subtracted	194.527	195.08	0.553
2507	5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196]
	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972]	Divided	151.386	151.009	1.0025
2508	calcium-binding mitochondrial carrier protein aralar2 (solute carrier family 25, member 13) (citrin). [swissprot;acc:q9ujs0]	Subtracted	194.527	195.08	0.553
	cerebral cell adhesion molecule. [refseq;acc:nm_016174]	Divided	194.349	193.871	1.00247
2509	acyl carrier protein, mitochondrial precursor (acp) (nadh-ubiquinone oxidoreductase 9.6 kda subunit) (ci-sdap). [swissprot;acc:o14561]	Subtracted	194.527	195.08	0.553
	chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [swissprot;acc:q13185]	Divided	187.902	188.366	1.00247
2510	grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5]		234.384	234.948	1.00241
	scribble. [refseq;acc:nm_015356]	Subtracted	221.782	222.291	0.509
2511	grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7]	Divided	234.384	234.948	1.00241
	lap (leucine-rich repeats and pdz) and no pdz protein. [refseq;acc:nm_018214]	Subtracted	221.776	222.283	0.507
2512	dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075]		215.835	216.341	0.506
	swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077]	Divided	234.384	234.948	1.00241
2513	adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [swissprot;acc:q9p2n4]	Subtracted	215.835	216.341	0.506
	swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078]	Divided	234.384	234.948	1.00241
2514	dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [swissprot;acc:o00273]	Subtracted	215.835	216.341	0.506
	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]	Divided	234.384	234.948	1.00241
2515	ankyrin 3 (ank-3) (ankyrin g). [swissprot;acc:q12955]	Subtracted	215.835	216.341	0.506
	dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075]	Divided			1.00234
2516	adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [swissprot;acc:q9p2n4]
	ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [swissprot;acc:q01484]	Subtracted			0.506
2517	adp-ribosylation factor-like protein 3. [swissprot;acc:p36405]
	dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [swissprot;acc:o00273]	Divided			1.00234
2518	ankyrin 3 (ank-3) (ankyrin g). [swissprot;acc:q12955]
	unc-119 protein homolog (retinal protein 4) (hrg4). [swissprot;acc:q13432]	Subtracted			0.506
2519	26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556]
	ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [swissprot;acc:q01484]	Divided			1.00234
2520	adp-ribosylation factor-like protein 3. [swissprot;acc:p36405]
	geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749]	Subtracted	236.51	236.008	0.502
2521	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Divided	201.96	201.488	1.00234
	transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854]	Subtracted	209.143	208.659	0.484
2522	cerebral cell adhesion molecule. [refseq;acc:nm_016174]		194.349	193.871	0.478
	unc-119 protein homolog (retinal protein 4) (hrg4). [swissprot;acc:q13432]	Divided	215.835	216.341	1.00234
2523	apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481]	Subtracted	216.264	215.787	0.477
	importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974]	Divided	201.96	201.488	1.00234
2524	proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [swissprot;acc:p28062]	Subtracted	212.464	211.99	0.474
	transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907]	Divided	201.96	201.488	1.00234
2525	26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556]		215.835	216.341
	chromobox protein homolog 5 (heterochromatin protein 1 homolog alpha) (hp1 alpha) (antigen p25). [swissprot;acc:p45973]	Subtracted	187.853	188.326	0.473
2526	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		201.96	201.488	0.472
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Divided			1.00234
2527	importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974]	Subtracted			0.472
	transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854]	Divided	209.143	208.659	1.00232
2528	scribble. [refseq;acc:nm_015356]		221.782	222.291	1.0023
	transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907]	Subtracted	201.96	201.488	0.472
2529	lap (leucine-rich repeats and pdz) and no pdz protein. [refseq;acc:nm_018214]	Divided	221.776	222.283	1.00229

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.