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

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Showing element 1375 to 1424 of 8289 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1

Rank	description	Interaction Map	red	green	network_comparison
688	dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514]	High confidence	237.554	250.823	1.05586
	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	Low confidence	216.552	210.641	1.02806
689	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]
	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	High confidence	135.379	128.225	1.05579
690	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Low confidence	216.552	210.641	1.02806
	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	High confidence	220.593	208.987	1.05553
691	atp-dependent helicase ddx8 (rna helicase hrh1) (deah-box protein 8). [swissprot;acc:q14562]	Low confidence	201.663	196.158	1.02806
	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872]	High confidence	217.602	206.195	1.05532
692	cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253]
	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55]	Low confidence	203.897	198.337	1.02803
693	adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377]		205.207	199.613	1.02802
	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513]	High confidence	222.554	234.847	1.05524
694	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519]	Low confidence	216.501	210.602	1.02801
	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864]	High confidence	241.907	229.35	1.05475
695	paxillin. [swissprot;acc:p49023]	Low confidence	202.649	197.13	1.028
	peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126]	High confidence	226.135	214.405	1.05471
696	interferon-related developmental regulator 1 (nerve growth factor- inducible protein pc4). [swissprot;acc:o00458]	Low confidence	204.538	198.974	1.02796
	sr rich protein. [refseq;acc:nm_032870]	High confidence	225.293	213.64	1.05455
697	chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]	Low confidence	202.744	197.238	1.02792
	ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794]	High confidence	220.444	209.113	1.05419
698	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478]		220.437	209.118	1.05413
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Low confidence	196.49	201.972	1.0279
699	adapter-related protein complex 1 sigma 1a subunit (sigma-adaptin 1a) (adaptor protein complex ap-1 sigma-1a subunit) (golgi adaptor ha1/ap1 adaptin sigma-1a subunit) (clathrin assembly protein complex 1 sigma- 1a small chain) (clathrin coat assembly protein ap19) (ha1 19 kda subunit) (sigma 1a subunit of ap-1 clathrin). [swissprot;acc:q00382]		205.169	199.601
	cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836]	High confidence	220.438	209.118	1.05413
700	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]
	wd-repeat protein 6. [swissprot;acc:q9nnw5]	Low confidence	204.863	199.304	1.02789
701	disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490]	High confidence	220.438	209.118	1.05413
	iron-responsive element binding protein 1 (ire-bp 1) (iron regulatory protein 1) (irp1) (ferritin repressor protein) (aconitate hydratase) (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:p21399]	Low confidence	200.577	195.136	1.02788
702	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865]	High confidence	220.438	209.118	1.05413
	ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283]	Low confidence	211.28	217.166	1.02786
703	limkain b1. [refseq;acc:nm_019081]	High confidence	220.438	209.118	1.05413
	periodic tryptophan protein 1 homolog (keratinocyte protein ief ssp 9502). [swissprot;acc:q13610]	Low confidence	203.581	198.065	1.02785
704	putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2]	High confidence	220.438	209.118	1.05413
	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333]	Low confidence	204.411	198.876	1.02783
705	cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851]	High confidence	220.438	209.118	1.05413
	spermatogenesis associated factor spaf. [refseq;acc:nm_145207]	Low confidence	205.124	199.576	1.0278
706	disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886]	High confidence	220.438	209.118	1.05413
	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4]	Low confidence	204.525	199.009	1.02772
707	dna replication factor; double parked, drosophila, homolog of. [refseq;acc:nm_030928]		204.969	199.442	1.02771
	kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042]	High confidence	220.438	209.118	1.05413
708	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]
	u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]	Low confidence	201.325	195.897	1.02771
709	ferritin light chain (ferritin l subunit). [swissprot;acc:p02792]	High confidence	220.438	209.118	1.05413
	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	Low confidence	204.178	198.675	1.0277
710	apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481]		202.569	197.109
	disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0]	High confidence	220.438	209.118	1.05413
711	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	Low confidence	198.97	193.609	1.02769
	tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577]	High confidence	232.468	245.048	1.05411
712	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]		220.431	209.123	1.05407
	gtp-binding protein sar1b. [swissprot;acc:q9y6b6]	Low confidence	201.401	195.979	1.02767

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.