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 4208 to 4257 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
2104	thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919]	Divided	209.328	207.813	1.00729
2105	adp-ribosylation factor 4. [swissprot;acc:p18085]	Subtracted	221.248	222.788	1.54
	eif-5a2 protein. [refseq;acc:nm_020390]	Divided	208.591	210.111	1.00729
2106	fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476]	Subtracted	221.248	222.788	1.54
	insulin gene enhancer protein isl-1 (islet-1). [swissprot;acc:p20663]	Divided	197.489	196.061	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]		216.23	217.801	1.00727
	shc transforming protein. [swissprot;acc:p29353]	Subtracted	221.248	222.788	1.54
2108	argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424]	Divided	216.36	217.93	1.00726
	zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [refseq;acc:nm_032389]	Subtracted	221.248	222.788	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	219.032	217.47	1.00718
2110	adp-ribosylation factor 1. [swissprot;acc:p32889]	Subtracted	221.248	222.788	1.54
	conserved oligomeric golgi complex component 6. [swissprot;acc:q9y2v7]	Divided	211.099	209.607	1.00712
2111	heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [swissprot;acc:p09651]	Subtracted	221.248	222.788	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	219.047	217.511	1.00706
2112	adp-ribosylation factor 3. [swissprot;acc:p16587]	Subtracted	221.248	222.788	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	223.415	224.989	1.00705
2113	protein sck (fragment). [swissprot;acc:p98077]	Subtracted	221.248	222.788	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	219.055	217.533	1.007
2114	heterogeneous nuclear ribonucleoproteins a2/b1 (hnrnp a2 / hnrnp b1). [swissprot;acc:p22626]	Subtracted	221.248	222.788	1.54
	triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098]	Divided	214.632	213.14	1.007
2115	ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2]
	ovarian carcinoma immunoreactive antigen. [refseq;acc:nm_017830]	Subtracted	221.248	222.788	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	214.632	213.14	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	221.248	222.788	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	214.632	213.14	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]		221.248	222.788	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	219.047	217.511	1.536
2120	eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159]		208.727	210.263
	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	221.248	222.788	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	219.055	217.533	1.522
2122	eif-5a2 protein. [refseq;acc:nm_020390]		208.591	210.111	1.52
	galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182]	Divided	206.473	207.911	1.00696
2123	adp-ribosylation factor 4. [swissprot;acc:p18085]		221.248	222.788
	thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919]	Subtracted	209.328	207.813	1.515
2124	calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797]		227.117	225.62	1.497
	fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476]	Divided	221.248	222.788	1.00696
2125	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	Subtracted	217.871	219.366	1.495
	shc transforming protein. [swissprot;acc:p29353]	Divided	221.248	222.788	1.00696
2126	40s ribosomal protein s7 (s8). [swissprot;acc:p23821]	Subtracted	217.871	219.366	1.495
	zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [refseq;acc:nm_032389]	Divided	221.248	222.788	1.00696
2127	26s proteasome-associated pad1 homolog. [refseq;acc:nm_005805]	Subtracted	217.871	219.366	1.495
	neuronal shc. [refseq;acc:nm_016848]	Divided	221.248	222.788	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	217.871	219.366	1.495
2129	heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [swissprot;acc:p09651]	Divided	221.248	222.788	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.