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	Network Comparison Type	Value Type	Interaction Map	Filtered	green	red	network_comparison

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Showing element 4208 to 4257 of 6456 in total

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

Rank	description	Network Comparison Type	green	red	network_comparison
2104	thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919]	Divided	207.813	209.328	1.00729
2105	adp-ribosylation factor 4. [swissprot;acc:p18085]	Subtracted	222.788	221.248	1.54
	eif-5a2 protein. [refseq;acc:nm_020390]	Divided	210.111	208.591	1.00729
2106	fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476]	Subtracted	222.788	221.248	1.54
	insulin gene enhancer protein isl-1 (islet-1). [swissprot;acc:p20663]	Divided	196.061	197.489	1.00728
2107	lim domain only 7; zinc-finger domain-containing protein; lomp protein; f-box only protein 20; f-box protein fbx20. [refseq;acc:nm_005358]		217.801	216.23	1.00727
	shc transforming protein. [swissprot;acc:p29353]	Subtracted	222.788	221.248	1.54
2108	argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424]	Divided	217.93	216.36	1.00726
	zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [refseq;acc:nm_032389]	Subtracted	222.788	221.248	1.54
2109	neuronal shc. [refseq;acc:nm_016848]
	ran-binding protein 2 (ranbp2) (nuclear pore complex protein nup358) (nucleoporin nup358) (358 kda nucleoporin) (p270). [swissprot;acc:p49792]	Divided	217.47	219.032	1.00718
2110	adp-ribosylation factor 1. [swissprot;acc:p32889]	Subtracted	222.788	221.248	1.54
	conserved oligomeric golgi complex component 6. [swissprot;acc:q9y2v7]	Divided	209.607	211.099	1.00712
2111	heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [swissprot;acc:p09651]	Subtracted	222.788	221.248	1.54
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	Divided	217.511	219.047	1.00706
2112	adp-ribosylation factor 3. [swissprot;acc:p16587]	Subtracted	222.788	221.248	1.54
	dna-directed rna polymerases iii 12.5 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c11 subunit) (hsc11p) (hrpc11) (my010 protein). [swissprot;acc:q9y2y1]	Divided	224.989	223.415	1.00705
2113	protein sck (fragment). [swissprot;acc:p98077]	Subtracted	222.788	221.248	1.54
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	Divided	217.533	219.055	1.007
2114	heterogeneous nuclear ribonucleoproteins a2/b1 (hnrnp a2 / hnrnp b1). [swissprot;acc:p22626]	Subtracted	222.788	221.248	1.54
	triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098]	Divided	213.14	214.632	1.007
2115	ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2]
	ovarian carcinoma immunoreactive antigen. [refseq;acc:nm_017830]	Subtracted	222.788	221.248	1.54
2116	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]
	lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571]	Divided	213.14	214.632	1.007
2117	seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81]
	solute carrier family 23, member 2 (sodium-dependent vitamin c transporter 2) (hsvct2) (na(+)/l-ascorbic acid transporter 2) (yolk sac permease-like molecule 2) (nucleobase transporter-like 1 protein). [swissprot;acc:q9ugh3]	Subtracted	222.788	221.248	1.54
2118	dual specificity mitogen-activated protein kinase kinase 7 (ec 2.7.1.-) (map kinase kinase 7) (mapkk 7) (mapk/erk kinase 7) (jnk activating kinase 2) (c-jun n-terminal kinase kinase 2) (jnk kinase 2) (jnkk 2). [swissprot;acc:o14733]
	seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591]	Divided	213.14	214.632	1.007
2119	potassium channel modulatory factor 1; potassium channel modulatory factor; differentially expressed in branching tubulogenesis 91; zinc finger, zz domain containing 1. [refseq;acc:nm_020122]		222.788	221.248	1.00696
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	Subtracted	217.511	219.047	1.536
2120	eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159]		210.263	208.727
	solute carrier family 23, member 1 (sodium-dependent vitamin c transporter 1) (hsvct1) (na(+)/l-ascorbic acid transporter 1) (yolk sac permease-like molecule 3). [swissprot;acc:q9uhi7]	Divided	222.788	221.248	1.00696
2121	heterogeneous nuclear ribonucleoprotein a3 (hnrnp a3) (d10s102). [swissprot;acc:p51991]
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	Subtracted	217.533	219.055	1.522
2122	eif-5a2 protein. [refseq;acc:nm_020390]		210.111	208.591	1.52
	galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182]	Divided	207.911	206.473	1.00696
2123	adp-ribosylation factor 4. [swissprot;acc:p18085]		222.788	221.248
	thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919]	Subtracted	207.813	209.328	1.515
2124	calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797]		225.62	227.117	1.497
	fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476]	Divided	222.788	221.248	1.00696
2125	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	Subtracted	219.366	217.871	1.495
	shc transforming protein. [swissprot;acc:p29353]	Divided	222.788	221.248	1.00696
2126	40s ribosomal protein s7 (s8). [swissprot;acc:p23821]	Subtracted	219.366	217.871	1.495
	zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [refseq;acc:nm_032389]	Divided	222.788	221.248	1.00696
2127	26s proteasome-associated pad1 homolog. [refseq;acc:nm_005805]	Subtracted	219.366	217.871	1.495
	neuronal shc. [refseq;acc:nm_016848]	Divided	222.788	221.248	1.00696
2128	adp-ribosylation factor 1. [swissprot;acc:p32889]
	apolipoprotein b-100 precursor (apo b-100) [contains: apolipoprotein b-48 (apo b-48)]. [swissprot;acc:p04114]	Subtracted	219.366	217.871	1.495
2129	heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [swissprot;acc:p09651]	Divided	222.788	221.248	1.00696

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.