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

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Showing element 2730 to 2779 of 3228 in total

Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

description	Rank	red	green	network_comparison
succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597]	2503	5996.06	6155.81	1.02664
suppressor of actin 1. [refseq;acc:nm_014016]	2826	0.00001	0.00001	1
suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553]	2622	5599.85	5683	1.01485
suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524]	1204	5946.33	6459.79	1.08635
suppressor of fused. [refseq;acc:nm_016169]	1185	4392.63	4776.19	1.08732
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55]	437	3779.92	4348.48	1.15042
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	2380	3690.79	3543.33	1.04162
suppressor of var1, 3-like 1. [refseq;acc:nm_003171]	1321	6439.79	6959.21	1.08066
surfeit locus protein 1. [swissprot;acc:q15526]	929	5638.46	6194.04	1.09853
surfeit locus protein 5. [swissprot;acc:q15528]	2229	3650.8	3484.94	1.04759
survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637]	1996	5047.2	5344.68	1.05894
survival of motor neuron protein-interacting protein 1 (smn- interacting protein 1) (component of gems 2) (gemin2). [swissprot;acc:o14893]	2002
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824]	1153	5840.01	6355.56	1.08828
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]	572	4134.77	4691.24	1.13458
swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601]	2053	5634.8	5952.7	1.05642
swi/snf-related matrix-associated actin-dependent regulator of chromatin c1; mammalian chromatin remodeling complex brg1-associated factor 155; swi/snf complex 155 kda subunit; chromatin remodeling complex baf155 subunit. [refseq;acc:nm_003074]	2063	5634.63	5952.14	1.05635
swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075]	2049	5634.94	5953.19	1.05648
swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077]	570	4134.77	4691.24	1.13458
swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078]	571
swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497]	438	6252.58	7192.88	1.15039
symplekin. [swissprot;acc:q92797]	601	15213.4	13418.1	1.1338
synapsin i (brain protein 4.1). [swissprot;acc:p17600]	1021	5791.82	6340.86	1.0948
synapsin ii. [swissprot;acc:q92777]	1014
synapsin iii. [swissprot;acc:o14994]	1009
synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721]	2724	5603.24	5583.64	1.00351
synaptotagmin xii (sytxii). [swissprot;acc:q8iv01]	1105	5460.49	5954.62	1.09049
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	351	17396.9	20483.9	1.17745
syndecan-3 (synd3). [swissprot;acc:o75056]	2862	0.00001	0.00001	1
syntaxin 10 (syn10). [swissprot;acc:o60499]	2750	5294.28	5298.42	1.00078
syntaxin 12. [refseq;acc:nm_177424]	682	5552.92	6217.59	1.1197
syntaxin 16 (syn16). [swissprot;acc:o14662]	2719	5603.24	5583.64	1.00351
syntaxin 18. [swissprot;acc:q9p2w9]	1965	4374.32	4126.96	1.05994
syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]	2721	5603.24	5583.64	1.00351
syntaxin 1b. [swissprot;acc:q15531]	2725
syntaxin 5. [swissprot;acc:q13190]	2866	0.00001	0.00001	1
syntaxin 6. [swissprot;acc:o43752]	2748	5296.39	5301.11	1.00089
syntaxin 7. [swissprot;acc:o15400]	721	5580.97	6233.52	1.11692
t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [swissprot;acc:o43435]	2771	0.00001	0.00001	1
t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806]	1632	6179.59	6613.15	1.07016
t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947]	2697	5176.92	5154.43	1.00436
t-cell activation wd repeat protein. [refseq;acc:nm_139281]	831	4062.03	4492.48	1.10597
t-cell acute lymphocytic leukemia-1 protein (tal-1 protein) (stem cell protein) (t-cell leukemia/lymphoma-5 protein). [swissprot;acc:p17542]	2865	0.00001	0.00001	1
t-cell acute lymphocytic leukemia-2 protein (tal-2 protein). [swissprot;acc:q16559]	2760
t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314]	2568	3964.71	4042.75	1.01968
t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763]	2567
t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711]	2564
t-complex 11. [refseq;acc:nm_018679]	2392	6327.14	6579.38	1.03987
t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808]	1370	10231.8	9487.34	1.07847
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	356	11004.2	12944.2	1.1763
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	201	4810.22	6075.04	1.26294

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.