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

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Showing element 451 to 500 of 77072 in total

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

description	Interaction Map	Rank
ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]	High confidence	2895
ring finger protein 3. [refseq;acc:nm_006315]		2763
ring finger protein 4. [swissprot;acc:p78317]		3189
rna-binding protein 8a (rna binding motif protein 8a) (ribonucleoprotein rbm8a) (rna-binding protein y14) (binder of ovca1- 1) (bov-1). [swissprot;acc:q9y5s9]		2996
rp42 homolog; squamous cell carcinoma-related oncogene. [refseq;acc:nm_020640]		3198
runt-related transcription factor 1 (core-binding factor, alpha 2 subunit) (cbf-alpha 2) (acute myeloid leukemia 1 protein) (oncogene aml-1) (polyomavirus enhancer binding protein 2 alpha b subunit) (pebp2-alpha b) (pea2-alpha b) (sl3-3 enhancer factor 1 alpha b subunit) (sl3/akv core-binding factor alpha b subunit). [swissprot;acc:q01196]		2877
	Low confidence	5027
runt-related transcription factor 3 (core-binding factor, alpha 3 subunit) (cbf-alpha 3) (acute myeloid leukemia 2 protein) (oncogene aml-2) (polyomavirus enhancer binding protein 2 alpha c subunit) (pebp2-alpha c) (pea2-alpha c) (sl3-3 enhancer factor 1 alpha c subunit) (sl3/akv core-binding factor alpha c subunit). [swissprot;acc:q13761]	High confidence	3208
	Low confidence	5061
rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]	High confidence	3073
sam domain and hd domain-containing protein 1 (dendritic cell-derived ifng-induced protein) (dcip) (monocyte protein 5) (mop-5). [swissprot;acc:q9y3z3]		3124
	Low confidence	5051
schwannomin interacting protein 1. [refseq;acc:nm_014575]	High confidence	2900
sec23-interacting protein p125; phospholipase. [refseq;acc:nm_007190]		3097
semaphorin 6b precursor (semaphorin z) (sema z). [swissprot;acc:q9h3t3]		2832
semaphorin 6c precursor (semaphorin y) (sema y). [swissprot;acc:q9h3t2]		2933
semaphorin 6d isoform 3 precursor. [refseq;acc:nm_153617]		2964
sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8]		2843
serine/threonine kinase 38 like. [refseq;acc:nm_015000]		2897
serine/threonine kinase 38; serine threonine protein kinase. [refseq;acc:nm_007271]		3071
serine/threonine protein kinase 24 (ec 2.7.1.37) (ste20-like kinase mst3) (mst-3) (mammalian ste20-like protein kinase 3). [swissprot;acc:q9y6e0]		3115
serine/threonine protein kinase 25 (ec 2.7.1.37) (sterile 20/oxidant stress-response kinase 1) (ste20/oxidant stress response kinase-1) (sok-1) (ste20-like kinase). [swissprot;acc:o00506]		3048
serine/threonine protein kinase 3 (ec 2.7.1.37) (ste20-like kinase mst2) (mst-2) (mammalian ste20-like protein kinase 2) (serine/threonine protein kinase krs-1). [swissprot;acc:q13188]		3111
serine/threonine protein kinase mask; ste20-like kinase mst4. [refseq;acc:nm_016542]		2982
serine/threonine-protein kinase chk1 (ec 2.7.1.-). [swissprot;acc:o14757]		2908
serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532]		3137
serine/threonine-protein kinase receptor r3 precursor (ec 2.7.1.37) (skr3) (activin receptor-like kinase 1) (alk-1) (tgf-b superfamily receptor type i) (tsr-i). [swissprot;acc:p37023]		2952
set protein (hla-dr associated protein ii) (phapii) (phosphatase 2a inhibitor i2pp2a). [swissprot;acc:q01105]		3039
sex comb on midleg homolog 1. [refseq;acc:nm_012236]		3217
sex comb on midleg-like 2; sex comb on midleg like 2. [refseq;acc:nm_006089]		3120
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]		2794
sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]		2867
signal recognition particle 14 kda protein (srp14) (18 kda alu rna binding protein). [swissprot;acc:p37108]	Low confidence	5033
similar to cg5057 gene product. [sptrembl;acc:q9btt4]	High confidence	2984
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]		3032
similar to mob-lak. [refseq;acc:nm_145279]		2937
skd1 protein (vacuolar sorting protein 4b). [swissprot;acc:o75351]		3037
skeletal muscle and kidney enriched inositol phosphatase isoform 1; 43-kda form skeletal muscle and kidney enriched inositol phosphatase. [refseq;acc:nm_016532]		2994
small edrk-rich factor 2. [refseq;acc:nm_005770]		2947
small nuclear ribonucleoprotein associated protein n (snrnp-n) (sm protein n) (sm-n) (smn) (sm-d) (tissue-specific splicing protein). [swissprot;acc:p14648]		3004
small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]		3012
snrna activating protein complex 50 kda subunit (snapc 50 kda subunit) (proximal sequence element-binding transcription factor beta subunit) (pse-binding factor beta subunit) (ptf beta subunit). [swissprot;acc:q92966]		2849
solute carrier family 21 member 15 (organic anion transporter polypeptide-related protein 4) (oatp-rp4) (oatprp4). [swissprot;acc:q9h2y9]		2965
	Low confidence	5035
solute carrier family 36 member 1; proton / amino acid symporter; lysosomal amino acid transporter 1. [refseq;acc:nm_078483]	High confidence	3026
sorting nexin 16. [swissprot;acc:p57768]		3108
sparc precursor (secreted protein acidic and rich in cysteine) (osteonectin) (on) (basement membrane protein bm-40). [swissprot;acc:p09486]		3062
sparc-like protein 1 precursor (high endothelial venule protein) (hevin) (mast 9). [swissprot;acc:q14515]		2899
spartin; trans-activated by hepatitis c virus core protein 1. [refseq;acc:nm_015087]		2987
speckle-type poz protein. [swissprot;acc:o43791]		3031

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.