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

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Showing element 3958 to 4007 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
1979	tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530]	Divided	209.539	207.529	1.00969
1980	solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330]	Subtracted	191.406	193.385	1.979
	tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5]	Divided	209.539	207.529	1.00969
1981	d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175]
	disrupter of silencing 10. [refseq;acc:nm_020368]	Subtracted	191.411	193.39	1.979
1982	40s ribosomal protein s28. [swissprot;acc:p25112]	Divided	200.343	198.427	1.00966
	very long-chain acyl-coa synthetase homolog 1. [refseq;acc:nm_014031]	Subtracted	191.41	193.389	1.979
1983	lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457]	Divided	219.25	217.175	1.00955
	solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [refseq;acc:nm_012254]	Subtracted	191.408	193.387	1.979
1984	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	Divided	219.26	217.193	1.00952
	similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4]	Subtracted	191.415	193.394	1.979
1985	lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362]		225.015	223.041	1.974
	mitochondrial ribosomal protein l24. [refseq;acc:nm_024540]	Divided	219.26	217.193	1.00952
1986	65 kda yes-associated protein (yap65). [swissprot;acc:p46937]
	blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161]	Subtracted	196.964	198.935	1.971
1987	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]
	lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664]	Divided	225.022	222.9	1.00952
1988	9 kda protein. [swissprot;acc:p13994]		219.26	217.193
	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]	Subtracted	196.965	198.936	1.971
1989	collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955]	Divided	219.261	217.195	1.00951
	protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481]	Subtracted	217.662	215.693	1.969
1990	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	Divided	219.26	217.194	1.00951
	protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480]	Subtracted	217.676	215.709	1.967
1991	dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472]		217.941	215.979	1.962
	transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472]	Divided	219.26	217.194	1.00951
1992	proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [swissprot;acc:p40306]	Subtracted	216.201	214.245	1.956
	zasp protein (fragment). [sptrembl;acc:q9y4z3]	Divided	219.267	217.207	1.00948
1993	creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [swissprot;acc:p17540]	Subtracted	198.3	196.347	1.953
	huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146]	Divided	189.052	190.835	1.00943
1994	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532]	Subtracted	198.293	196.341	1.952
	goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4]	Divided	189.011	190.787	1.0094
1995	huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291]		188.961	190.73	1.00936
	peptidyl prolyl isomerase h; cyclophilin h. [refseq;acc:nm_006347]	Subtracted	198.258	196.319	1.939
1996	prp18 pre-mrna processing factor 18 homolog. [refseq;acc:nm_003675]
	sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911]	Divided	204.682	202.784	1.00936
1997	j domain protein c21orf55. [swissprot;acc:q9nx36]	Subtracted	198.257	196.319	1.938
	kidney and liver proline oxidase 1. [refseq;acc:nm_021232]	Divided	204.651	202.759	1.00933
1998	creatine kinase, b chain (ec 2.7.3.2) (b-ck). [swissprot;acc:p12277]	Subtracted	198.19	196.252	1.938
	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304]	Divided	200.219	198.37	1.00932
1999	acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954]	Subtracted	215.799	213.865	1.934
	solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913]	Divided	204.636	202.748	1.00931
2000	40s ribosomal protein s28. [swissprot;acc:p25112]	Subtracted	200.343	198.427	1.916
	sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289]	Divided	204.626	202.739	1.00931
2001	creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732]	Subtracted	198.258	196.346	1.912
	lin-7 homolog b; lin-7b protein; likely ortholog of mouse lin-7b; mammalian lin-7 protein 2; likely orholog of mouse lin 7 homolog b (c. elegans). [refseq;acc:nm_022165]	Divided	225.02	222.948	1.00929
2002	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645]	Subtracted	208.315	206.41	1.905
	u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579]	Divided	214.775	216.769	1.00928
2003	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645]		208.315	206.41	1.00923
	traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614]	Subtracted	218.466	216.562	1.904
2004	proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004]		229.102	231.001	1.899

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.