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

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Showing element 1 to 50 of 38536 in total

Value Type  : Measured
Interaction Map  : High confidence
Network Comparison Type  : Divided
green  : 0.00001
red  : 0.00001
network_comparison  : 1

description	Rank	Filtered
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 4 (ec 3.1.4.11) (phosphoinositide phospholipase c) (plc-beta-4) (phospholipase c-beta-4). [swissprot;acc:q15147]	3126	1
10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891]	2922
14-3-3 protein epsilon (mitochondrial import stimulation factor l subunit) (protein kinase c inhibitor protein-1) (kcip-1) (14-3-3e). [swissprot;acc:p42655]	3088
15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [swissprot;acc:p15428]	2855
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	3079
3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [refseq;acc:nm_025193]	3147
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	2756
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]	2802
3-hydroxyacyl-coa dehydrogenase type ii (ec 1.1.1.35) (type ii hadh) (endoplasmic reticulum-associated amyloid beta-peptide binding protein) (short-chain type dehydrogenase/reductase xh98g2). [swissprot;acc:q99714]	3180
6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [swissprot;acc:q03393]	2904
60s ribosomal protein l37a. [swissprot;acc:p12751]	2959
69 kda islet cell autoantigen (ica69) (islet cell autoantigen 1) (islet cell autoantigen p69) (icap69). [swissprot;acc:q05084]	3227
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]	2788
activin receptor type i precursor (ec 2.7.1.37) (actr-i) (serine/threonine-protein kinase receptor r1) (skr1) (activin receptor-like kinase 2) (alk-2) (tgf-b superfamily receptor type i) (tsr-i). [swissprot;acc:q04771]	3050
adaptor protein with pleckstrin homology and src homology 2 domains. [refseq;acc:nm_020979]	2870
aldehyde dehydrogenase 7 (ec 1.2.1.5). [swissprot;acc:p43353]	3222
aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]	2992
aldehyde oxidase (ec 1.2.3.1). [swissprot;acc:q06278]	2960
alpha crystallin a chain. [swissprot;acc:p02489]	2875
alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511]	3082
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]	2829
amyloid beta precursor protein-binding protein 2; amyloid beta precursor protein (cytoplasmic tail)-binding protein 2; protein interacting with app tail 1. [refseq;acc:nm_006380]	3191
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]	2798
atp synthase coupling factor 6, mitochondrial precursor (ec 3.6.3.14) (f6). [swissprot;acc:p18859]	2893
atp synthase g chain, mitochondrial (ec 3.6.3.14) (atpase subunit g). [swissprot;acc:o75964]	2834
au rna-binding protein/enoyl-coenzyme a hydratase precursor; au rna-binding protein/enoyl-coenzyme a hydratase; 3-methylglutaconyl-coa hydratase; mga type i. [refseq;acc:nm_001698]	2913
ba203i16.1 (hypothetical protein kiaa0970). [sptrembl;acc:q9h1w1]	3117
ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [sptrembl;acc:q9bx39]	2968
barrier-to-autointegration factor (breakpoint cluster region protein 1). [swissprot;acc:o75531]	2804
bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [swissprot;acc:p55061]	2950
bcl-6 interacting corepressor isoform 1. [refseq;acc:nm_017745]	2776
beta-ureidopropionase (ec 3.5.1.6) (beta-alanine synthase) (n-carbamoyl-beta-alanine amidohydrolase) (bup-1). [swissprot;acc:q9ubr1]	3145
bone morphogenetic protein 5 precursor (bmp-5). [swissprot;acc:p22003]	3069
bone morphogenetic protein 6 precursor (bmp-6). [swissprot;acc:p22004]	2896
bone morphogenetic protein 7 precursor (bmp-7) (osteogenic protein 1) (op-1). [swissprot;acc:p18075]	3128
bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]	2773
brca1 associated protein. [refseq;acc:nm_006768]	502	0
	3161	1
bromodomain and phd finger-containing protein 3 (fragment). [swissprot;acc:q9uld4]	3149
bromodomain-containing protein 1 (br140-like protein). [swissprot;acc:o95696]	3139
bs4 protein (ny-ren-18 antigen). [swissprot;acc:q9y5a7]	3214
bup protein. [refseq;acc:nm_012071]	2911
calmodulin. [swissprot;acc:p02593]	2928
camp responsive element binding protein-like 2. [refseq;acc:nm_001310]	3078
camp-dependent protein kinase type i-alpha regulatory chain (tissue- specific extinguisher-1) (tse1). [swissprot;acc:p10644]	3089
carcinoma related gene. [refseq;acc:nm_016041]	3179
carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [swissprot;acc:p23786]	2885
casein kinase i, gamma 1 isoform (ec 2.7.1.-) (cki-gamma 1). [swissprot;acc:q9hcp0]	2830
casein kinase i, gamma 2 isoform (ec 2.7.1.-) (cki-gamma 2). [swissprot;acc:p78368]	2986
casein kinase i, gamma 3 isoform (ec 2.7.1.-) (cki-gamma 3). [swissprot;acc:q9y6m4]	2901

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.