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

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Showing element 451 to 500 of 77072 in total

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

description	Interaction Map	Rank
solute carrier family 21 member 15 (organic anion transporter polypeptide-related protein 4) (oatp-rp4) (oatprp4). [swissprot;acc:q9h2y9]	High confidence	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
spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]		3038
sperm tail protein shippo1; h-shippo 1. [refseq;acc:nm_053280]		2797
spermine synthase (ec 2.5.1.22) (spermidine aminopropyltransferase) (spmsy). [swissprot;acc:p52788]		3118
spinster-like protein. [sptrembl;acc:q9h2v7]	Low confidence	5024
spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	High confidence	2879
spry domain-containing socs box protein ssb-1. [refseq;acc:nm_025106]		2814
spry domain-containing socs box protein ssb-4. [refseq;acc:nm_080862]		2806
ss18-like protein 1 (syt homolog-1). [swissprot;acc:o75177]		2766
ssxt protein (synovial sarcoma, translocated to x chromosome) (syt protein). [swissprot;acc:q15532]		2942
ste20-like kinase; ste2-like kinase. [refseq;acc:nm_016281]		2980
steroidogenic factor 1 (stf-1) (sf-1) (steroid hormone receptor ad4bp) (fushi tarazu factor homolog 1). [swissprot;acc:q13285]		2972
suppressor of actin 1. [refseq;acc:nm_014016]		2826
syndecan-3 (synd3). [swissprot;acc:o75056]		2862
syntaxin 5. [swissprot;acc:q13190]		2866
t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [swissprot;acc:o43435]		2771
t-cell acute lymphocytic leukemia-1 protein (tal-1 protein) (stem cell protein) (t-cell leukemia/lymphoma-5 protein). [swissprot;acc:p17542]		2865
t-cell acute lymphocytic leukemia-2 protein (tal-2 protein). [swissprot;acc:q16559]		2760
t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227]		2917
t-complex protein 1, zeta-2 subunit (tcp-1-zeta-2) (cct-zeta-2) (tcp- 1-zeta-like) (cct-zeta-like) (testis-specific tcp20) (testis-specific protein tsa303). [swissprot;acc:q92526]		2995
taube nuss. [refseq;acc:nm_138572]		2967
tektin 2 (tektin-t) (testicular tektin b1-like protein). [swissprot;acc:q9uif3]		3156
testis intracellular mediator protein. [refseq;acc:nm_057161]		3019
testis specific leucine rich repeat protein. [refseq;acc:nm_012472]		3003
	Low confidence	5039
testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562]	High confidence	3021
tetratricopeptide repeat protein 1 (tpr repeat protein 1). [swissprot;acc:q99614]		3060
thousand and one amino acid protein kinase. [refseq;acc:nm_004783]		2906
thymidine kinase 2, mitochondrial precursor (ec 2.7.1.21) (mt-tk). [swissprot;acc:o00142]		2837
	Low confidence	5025
tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	High confidence	2816
	Low confidence	5023
tigger transposable element derived 6. [refseq;acc:nm_030953]	High confidence	2853
	Low confidence	5026
tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	High confidence	2944
	Low confidence	5032
trabid protein. [swissprot;acc:q9ugi0]	High confidence	3210
transcription factor 12 (transcription factor htf-4) (e-box-binding protein) (dna-binding protein htf4). [swissprot;acc:q99081]		2948
transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]		2940
transcription factor ap-2 alpha (ap2-alpha) (activating enhancer- binding protein 2 alpha) (ap-2 transcription factor) (activator protein-2) (ap-2). [swissprot;acc:p05549]		2969
transcription factor ap-2 beta (ap2-beta) (activating enhancer-binding protein 2 beta). [swissprot;acc:q92481]		3220
transcription factor ap-2 gamma (ap2-gamma) (activating enhancer- binding protein 2 gamma) (transcription factor erf-1). [swissprot;acc:q92754]		3164
transcription factor e2-alpha (immunoglobulin enhancer binding factor e12/e47) (transcription factor-3) (tcf-3) (immunoglobulin transcription factor-1) (transcription factor itf-1) (kappa-e2-binding factor). [swissprot;acc:p15923]		3182

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.