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

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Showing element 601 to 650 of 77072 in total

Value Type  : Measured
green  : 0.00001
Filtered  : 1
network_comparison  : 1
red  : 0.00001
Network Comparison Type  : Divided

description	Interaction Map	Rank
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]	High confidence	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]		3161
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
	Low confidence	5058
carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [swissprot;acc:p23786]	High confidence	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
caveolin-1. [swissprot;acc:q03135]		3099
caveolin-3 (m-caveolin). [swissprot;acc:p56539]		2779
ccr4-not transcription complex, subunit 3; not3 (negative regulator of transcription 3, yeast) homolog. [refseq;acc:nm_014516]		3163
ccr4-not transcription complex, subunit 6-like. [refseq;acc:nm_144571]		2958
ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]		3226
ccr4-not transcription complex, subunit 8 (caf1-like protein) (califp). [swissprot;acc:q9uff9]		2890
cdk-activating kinase assembly factor mat1 (ring finger protein mat1) (menage a trois) (cdk7/cyclin h assembly factor) (p36) (p35) (cyclin g1 interacting protein). [swissprot;acc:p51948]		3209
cell division protein kinase 5 (ec 2.7.1.-) (tau protein kinase ii catalytic subunit) (tpkii catalytic subunit) (serine/threonine protein kinase pssalre). [swissprot;acc:q00535]		2850
cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]		2990
cell division protein kinase 9 (ec 2.7.1.-) (serine/threonine-protein kinase pitalre) (c-2k). [swissprot;acc:p50750]		2974
centromere/kinetochore protein zw10 homolog. [swissprot;acc:o43264]		3167
cisplatin resistance related protein crr9p. [refseq;acc:nm_030782]		3197
cleavage stimulation factor, 50 kda subunit (cstf 50 kda subunit) (cf-1 50 kda subunit). [swissprot;acc:q05048]		3129
clll6 protein. [refseq;acc:nm_020456]		3028
cobw-like protein. [refseq;acc:nm_018491]	Low confidence	5031
collectin sub-family member 12 isoform i; scavenger receptor with c-type lectin; collectin placenta 1; scavenger receptor class a, member 4. [refseq;acc:nm_130386]	High confidence	2881
	Low confidence	5028
complement component c6 precursor. [swissprot;acc:p13671]	High confidence	3199
complement component c7 precursor. [swissprot;acc:p10643]		3064
complement component c8 alpha chain precursor. [swissprot;acc:p07357]		2886
complement component c8 beta chain precursor. [swissprot;acc:p07358]		3207
complement component c9 precursor. [swissprot;acc:p02748]		3057
connective tissue growth factor precursor (hypertrophic chondrocyte- specific protein 24). [swissprot;acc:p29279]		3040
connective tissue growth factor-like protein precursor (ctgf-l) (wnt1 inducible signaling pathway protein 2) (wisp-2) (connective tissue growth factor-related protein 58). [swissprot;acc:o76076]		3188
conserved oligomeric golgi complex component 1. [swissprot;acc:q8wtw3]		2836

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.