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

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Showing element 401 to 450 of 77072 in total

green  : 0
Filtered  : 1
Value Type  : Measured
network_comparison  : 0
Network Comparison Type  : Subtracted
red  : 0

description	Interaction Map	Rank
protein c20orf24 (rab5-interacting protein) (rip5) (pnas-11). [swissprot;acc:q9buv8]	High confidence	3131
protein c20orf43 (hspc164/hspc169) (ad-007) (cda05). [swissprot;acc:q9by42]		3206
protein c21orf2 (c21orf-humf09g8.5) (yf5/a2). [swissprot;acc:o43822]		2874
protein c6orf55 (dopamine responsive protein drg-1) (my012 protein) (hspc228). [swissprot;acc:q9np79]		3219
protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284]		3102
protein kinase c and casein kinase substrate in neurons protein 1. [swissprot;acc:q9by11]		3020
protein kinase c and casein kinase substrate in neurons protein 2. [swissprot;acc:q9unf0]		3142
protein kinase c and casein kinase substrate in neurons protein 3 (sh3 domain-containing protein 6511) (endophilin i). [swissprot;acc:q9uks6]		2845
protein kinase c, delta type (ec 2.7.1.-) (npkc-delta). [swissprot;acc:q05655]		2857
protein kinase c, theta type (ec 2.7.1.-) (npkc-theta). [swissprot;acc:q04759]		3186
protein transport protein sec23a (sec23-related protein a). [swissprot;acc:q15436]		3135
protein transport protein sec23b (sec23-related protein b). [swissprot;acc:q15437]		3127
protein transport protein sec24a (sec24-related protein a) (fragment). [swissprot;acc:o95486]		3056
protein transport protein sec24b (sec24-related protein b). [swissprot;acc:o95487]		2956
protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]		2910
protein transport protein sec24d (sec24-related protein d). [swissprot;acc:o94855]		2903
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]		2789
protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]		2838
protoporphyrinogen oxidase (ec 1.3.3.4) (ppo). [swissprot;acc:p50336]		2934
ptd016 protein. [refseq;acc:nm_016125]		3093
putative membrane protein. [refseq;acc:nm_019026]		2935
putative mitochondrial solute carrier; hypothetical protein npd016; putative mitochondrial solute carrier. [refseq;acc:nm_031212]		2891
putative nadh oxidoreductase complex i subunit homolog. [sptrembl;acc:q96q80]		3146
	Low confidence	5056
putative tumor suppressor 101f6. [refseq;acc:nm_007022]	High confidence	3051
	Low confidence	5046
r3h domain (binds single-stranded nucleic acids) containing-like. [refseq;acc:nm_178491]	High confidence	3132
rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]		3119
rab gdp dissociation inhibitor beta (rab gdi beta) (gdi-2). [swissprot;acc:p50395]		3193
rab geranylgeranyltransferase alpha subunit (ec 2.5.1.-) (rab geranyl- geranyltransferase alpha subunit) (rab gg transferase alpha) (rab ggtase alpha). [swissprot;acc:q92696]		3134
rala binding protein 1; rala-binding protein. [refseq;acc:nm_006788]		3212
ran binding protein 3 isoform ranbp3-d; ran-binding protein-3. [refseq;acc:nm_007322]		3202
rap1 gtpase-gdp dissociation stimulator 1 (smg p21 stimulatory gdp/gtp exchange protein) (smg gds protein) (exchange factor smggds). [swissprot;acc:p52306]	Low confidence	5034
ras-related protein rab-11a (rab-11) (24kg) (yl8). [swissprot;acc:p24410]	High confidence	3112
ras-related protein rab-11b (gtp-binding protein ypt3). [swissprot;acc:q15907]		2764
ras-related protein rab-1a (ypt1-related protein). [swissprot;acc:p11476]		2961
ras-related protein rab-1b. [swissprot;acc:q9h0u4]		2807
ras-related protein rab-2a. [swissprot;acc:p08886]		3110
ras-related protein ral-a. [swissprot;acc:p11233]		3223
ras-related protein ral-b. [swissprot;acc:p11234]		2925
rb1-inducible coiled coil protein 1. [refseq;acc:nm_014781]		3205
rcd1 required for cell differentiation1 homolog; protein involved in sexual development; rcd1 (required for cell differentiation, s.pombe) homolog 1. [refseq;acc:nm_005444]		2924
recessive polycystic kidney disease protein tg737 homolog. [swissprot;acc:q13099]		3201
regulatory protein tsc-22 (tgfb stimulated clone 22 homolog). [swissprot;acc:q15714]		3114
retinoic acid receptor rxr-alpha. [swissprot;acc:p19793]		2759
retinoic acid receptor rxr-beta. [swissprot;acc:p28702]		3067
retinoic acid receptor rxr-gamma. [swissprot;acc:p48443]		2936
ribonuclease iii (ec 3.1.26.3) (rnase iii) (p241). [swissprot;acc:q9nrr4]		3059
ribose-phosphate pyrophosphokinase i (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase i) (ppribp) (prs-i). [swissprot;acc:p09329]		2916
ribose-phosphate pyrophosphokinase ii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase ii) (ppribp) (prs-ii). [swissprot;acc:p11908]		3122

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.