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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Gene	Value Type	Rank	description	Network Comparison Type	Interaction Map	Filtered	green	red	network_comparison

Results: HTML CSV LaTeX

Showing element 51 to 100 of 1948 in total

Value Type  : Measured
Network Comparison Type  : Subtracted
Interaction Map  : High confidence
Filtered  : 1
green  : 0
red  : 0
network_comparison  : 0

Rank	description
2788	a-kinase anchor protein 5 (a-kinase anchor protein 79 kda) (akap 79) (camp-dependent protein kinase regulatory subunit ii high affinity binding protein) (h21). [swissprot;acc:p24588]
2789	protein-tyrosine phosphatase, non-receptor type 11 (ec 3.1.3.48) (protein-tyrosine phosphatase 2c) (ptp-2c) (ptp-1d) (sh-ptp3) (sh- ptp2) (shp-2). [swissprot;acc:q06124]
2790	transcription factor mafb (v-maf musculoaponeurotic fibrosarcoma oncogene homolog b). [swissprot;acc:q9y5q3]
2791	cytochrome c oxidase polypeptide va, mitochondrial precursor (ec 1.9.3.1). [swissprot;acc:p20674]
2792	transcription factor maf (proto-oncogene c-maf). [swissprot;acc:o75444]
2793	udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795]
2794	sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503]
2795	nadh-ubiquinone oxidoreductase 24 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3). [swissprot;acc:p19404]
2796	dna methyltransferase 1-associated protein 1 (dnmt1-associated protein 1) (dnmap1). [swissprot;acc:q9npf5]
2797	sperm tail protein shippo1; h-shippo 1. [refseq;acc:nm_053280]
2798	ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]
2799	hmg2 like. [refseq;acc:nm_145205]
2800	mondoa. [refseq;acc:nm_014938]
2801	dna-repair protein complementing xp-f cell (xeroderma pigmentosum group f complementing protein) (dna excision repair protein ercc-4). [swissprot;acc:q92889]
2802	3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [swissprot;acc:p14060]
2803	nanos (fragment). [sptrembl;acc:q8wy41]
2804	barrier-to-autointegration factor (breakpoint cluster region protein 1). [swissprot;acc:o75531]
2805	phosphofurin acidic cluster sorting protein 1 isoform 1; cytosolic sorting protein pacs-1. [refseq;acc:nm_018026]
2806	spry domain-containing socs box protein ssb-4. [refseq;acc:nm_080862]
2807	ras-related protein rab-1b. [swissprot;acc:q9h0u4]
2808	dna ligase iv (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p49917]
2809	polyhomeotic like 3; early development regulator 3; polyhomeotic 3. [refseq;acc:nm_024947]
2810	udp glycosyltransferase 2 family, polypeptide a1; udp glucuronosyltransferase 2 family, polypeptide a1. [refseq;acc:nm_006798]
2811	vascular endothelial growth factor b precursor (vegf-b) (vegf related factor) (vrf). [swissprot;acc:p49765]
2812	mob-lak. [refseq;acc:nm_130807]
2813	histone deacetylase 3 (hd3) (rpd3-2). [swissprot;acc:o15379]
2814	spry domain-containing socs box protein ssb-1. [refseq;acc:nm_025106]
2815	g protein-coupled receptor 66. [refseq;acc:nm_006056]
2816	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]
2817	tubulin-specific chaperone a (tubulin-folding cofactor a) (cfa) (tcp1-chaperonin cofactor a). [swissprot;acc:o75347]
2818	udp-glucuronosyltransferase 2b7 precursor, microsomal (ec 2.4.1.17) (udpgt) (3,4-catechol estrogen specific) (udpgth-2). [swissprot;acc:p16662]
2819	udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310]
2820	peregrin (bromodomain and phd finger-containing protein 1) (br140 protein). [swissprot;acc:p55201]
2821	vacuolar proton-atpase subunit. [sptrembl;acc:q8nhe4]
2822	zinc transporter 1 (znt-1). [swissprot;acc:q9y6m5]
2823	nuclear factor related to kappa b binding protein. [refseq;acc:nm_006165]
2824	heat-shock protein, beta-2 (hspb2) (dmpk-binding protein) (mkbp). [swissprot;acc:q16082]
2825	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]
2826	suppressor of actin 1. [refseq;acc:nm_014016]
2827	cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098]
2828	ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966]
2829	alveolar soft part sarcoma chromosome region, candidate 1; aspl protein; renal cell carcinoma gene on chromosome 17; renal cell carcinoma, papillary, 17 gene; aspscr1/tfe3 fusion gene, included. [refseq;acc:nm_024083]
2830	casein kinase i, gamma 1 isoform (ec 2.7.1.-) (cki-gamma 1). [swissprot;acc:q9hcp0]
2831	flap endonuclease-1 (ec 3.-.-.-) (maturation factor 1) (mf1). [swissprot;acc:p39748]
2832	semaphorin 6b precursor (semaphorin z) (sema z). [swissprot;acc:q9h3t3]
2833	tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226]
2834	atp synthase g chain, mitochondrial (ec 3.6.3.14) (atpase subunit g). [swissprot;acc:o75964]
2835	udp-glucuronosyltransferase 1-6 precursor, microsomal (ec 2.4.1.17) (udp-glucuronosyltransferase 1a6) (udpgt) (ugt1*6) (ugt1-06) (ugt1.6) (ugt-1f) (ugt1f) (phenol-metabolizing udp-glucuronosyltransferase). [swissprot;acc:p19224]
2836	conserved oligomeric golgi complex component 1. [swissprot;acc:q8wtw3]
2837	thymidine kinase 2, mitochondrial precursor (ec 2.7.1.21) (mt-tk). [swissprot;acc:o00142]

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.