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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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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 6712 to 6761 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	red	green	network_comparison
1678	serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [swissprot;acc:q9upe1]	Ranked	216.899	213.889	1.01407
1679	gtp binding protein 2. [refseq;acc:nm_019096]
	mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517]	Rooted	56.5094	58.3923	1.03332
	proteasome subunit beta type 3 (ec 3.4.25.1) (proteasome theta chain) (proteasome chain 13) (proteasome component c10-ii). [swissprot;acc:p49720]	Measured	6180.24	6608.11	1.06923
	suppressor of var1, 3-like 1. [refseq;acc:nm_003171]	Squared	31163.9	34454.3	1.10558
1680	bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933]
	cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941]	Ranked	216.899	213.889	1.01407
	methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898]	Measured	6436.73	6882.16	1.0692
	skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9]	Rooted	56.5094	58.3923	1.03332
1681	dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135]	Ranked	216.899	213.889	1.01407
	f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2]	Measured	6304.74	6740.66	1.06914
	glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840]	Squared	31163.9	34454.3	1.10558
	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]	Rooted	56.5094	58.3923	1.03332
1682	f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756]	Measured	6304.74	6740.66	1.06914
	glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841]	Squared	31163.9	34454.3	1.10558
	sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691]	Ranked	216.899	213.889	1.01407
	tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289]	Rooted	56.5094	58.3923	1.03332
1683	cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [swissprot;acc:p18850]	Ranked	216.899	213.889	1.01407
	dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	Squared	25120.7	27772.9	1.10558
	ring finger protein 20. [refseq;acc:nm_019592]	Measured	5419.54	5793.94	1.06908
	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]	Rooted	56.5094	58.3923	1.03332
1684	dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075]	Squared	27060.6	29916.8	1.10555
	neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1]	Rooted	56.5094	58.3923	1.03332
	ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [refseq;acc:nm_014771]	Measured	5419.54	5793.94	1.06908
	sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137]	Ranked	216.899	213.889	1.01407
1685	adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [swissprot;acc:q9p2n4]	Squared	27060.6	29916.8	1.10555
	gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6]	Measured	6088.07	6508.45	1.06905
	homeobox protein dlx-2. [swissprot;acc:q07687]	Rooted	56.5094	58.3923	1.03332
	xap-5 protein (hxc-26 protein). [swissprot;acc:q14320]	Ranked	216.899	213.889	1.01407
1686	dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [swissprot;acc:o00273]	Squared	27060.6	29916.8	1.10555
	homeobox protein dlx-5. [swissprot;acc:p56178]	Rooted	56.5094	58.3923	1.03332
	putative sialoglycoprotease type 2. [refseq;acc:nm_022353]	Ranked	220.75	217.704	1.01399
	toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603]	Measured	6088.07	6508.45	1.06905
1687	ankyrin 3 (ank-3) (ankyrin g). [swissprot;acc:q12955]	Squared	27060.6	29916.8	1.10555
	atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049]	Ranked	215.345	212.386	1.01393
	fetal brain protein 239 (239fb). [swissprot;acc:q15777]	Rooted	56.5094	58.3923	1.03332
	serpin b12. [swissprot;acc:q96p63]	Measured	5767.69	6165.87	1.06904
1688	ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [swissprot;acc:q01484]	Squared	27060.6	29916.8	1.10555
	homeobox protein dlx-3. [swissprot;acc:o60479]	Rooted	56.5094	58.3923	1.03332
	megsin (tp55) (serpin b7). [swissprot;acc:o75635]	Measured	5767.69	6165.87	1.06904
	transcription factor-like protein mrg15 (morf-related gene 15 protein) (mortality factor 4-like 1) (msl3-1 protein) (hspc008/hspc061). [swissprot;acc:q9ubu8]	Ranked	228.523	231.703	1.01392
1689	activated p21cdc42hs kinase. [refseq;acc:nm_005781]	Rooted	56.5094	58.3923	1.03332
	adp-ribosylation factor-like protein 3. [swissprot;acc:p36405]	Squared	27060.6	29916.8	1.10555
	dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0]	Ranked	228.277	225.163	1.01383
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Measured	5767.69	6165.87	1.06904
1690	40s ribosomal protein s24 (s19). [swissprot;acc:p16632]	Ranked	224.091	227.184	1.0138
	mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093]	Rooted	56.5094	58.3923	1.03332
	oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [swissprot;acc:p55055]	Measured	5767.69	6165.87	1.06904
	unc-119 protein homolog (retinal protein 4) (hrg4). [swissprot;acc:q13432]	Squared	27060.6	29916.8	1.10555
1691	26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556]

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.