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	Value Type	Gene	red	Rank	description	green	Interaction Map	network_comparison	Filtered

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Showing element 25276 to 25325 of 29840 in total

Network Comparison Type  : Subtracted
Value Type  : Squared
Interaction Map  : High confidence
Filtered  : 1

red	Rank	description	green	network_comparison
28982.3	508	peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521]	34012.8	5030.5
28990.9	436	sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289]	34656.4	5665.5
28992.5	1160	wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007]	32145.6	3153.1
28994.2	211	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	17134.8	11859.4
	212	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]
	213	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]
	214	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]
	215	protein hspc134 (protein cda04). [swissprot;acc:q9by43]
28995.9	1661	lamin a/c (70 kda lamin). [swissprot;acc:p02545]	31443.3	2447.4
28996.7	1662	centaurin beta 2 (cnt-b2). [swissprot;acc:q15057]	31444	2447.3
28996.8	1663	centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50]		2447.2
	1665	centaurin beta 1 (cnt-b1). [swissprot;acc:q15027]
28997.5	1664	lamin b1. [swissprot;acc:p20700]	31444.7
29012.2	498	testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8]	34163.9	5151.7
	499	chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824]
29012.4	500	testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7]	34164	5151.6
29016.1	497	chromodomain y-like protein 2. [refseq;acc:nm_152342]	34169.2	5153.1
29095.3	371	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632]	35337.6	6242.3
29095.7	370	grancalcin. [swissprot;acc:p28676]	35338.3	6242.6
29096	369	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	35338.7	6242.7
29098.8	368	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]	35342.6	6243.8
29101.9	366	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497]	35347	6245.1
	367	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]
29160.4	345	vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504]	35570.2	6409.8
29169.3	1983	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]	31251.6	2082.3
29173.8	495	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999]	34362.7	5188.9
29174	494	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749]	34363.5	5189.5
29224	501	glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057]	34362.1	5138.1
	502	proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272]
29238.6	1139	43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702]	32434.1	3195.5
29259.9	1122	lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362]	32490	3230.1
29261.2	1125	epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533]	32474.1	3212.9
	1126	receptor protein-tyrosine kinase erbb-2 precursor (ec 2.7.1.112) (p185erbb2) (neu proto-oncogene) (c-erbb-2) (tyrosine kinase-type cell surface receptor her2) (mln 19). [swissprot;acc:p04626]
	1127	receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303]	32473.8	3212.6
	1128	2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83]
	1129	receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860]
29261.6	1132	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]	32468.9	3207.3
29262.5	1137	lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664]	32458.3	3195.8
29263.6	1336	vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [swissprot;acc:p46459]	32125.4	2861.8
29291.1	1071	colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508]	32591.4	3300.3
29314.4	2211	glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448]	31053.9	1739.5
	2212	glutamate dehydrogenase 1, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p00367]
29333.2	1991	evolutionarily conserved signaling intermediate in toll pathway; ecsit. [refseq;acc:nm_016581]	31398.3	2065.1
29335.6	372	ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	35515.5	6179.9
29343.2	1626	proteasome subunit beta type 3 (ec 3.4.25.1) (proteasome theta chain) (proteasome chain 13) (proteasome component c10-ii). [swissprot;acc:p49720]	31849.8	2506.6
29345.2	1669	protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0]	31776.1	2430.9
29345.7	595	6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336]	34004.2	4658.5
29358.9	1398	proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [swissprot;acc:o14818]	32153.5	2794.6
29362.2	1399	proteasome subunit alpha type 7-like (ec 3.4.25.1). [swissprot;acc:q8taa3]	32156.5	2794.3
29406	1495	gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6]	32054.3	2648.3

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.