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 7362 to 7411 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
461	bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817]	Rooted	Subtracted	1	55.1867	60.5522	5.3655
	chromodomain y-like protein 2. [refseq;acc:nm_152342]	Squared	Divided	0	18606.3	18263.6	1.01876
	dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5]	Rooted	Subtracted		16.2959	16.5202	0.2243
	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	Measured	Divided		1915.69	1892.44	1.01229
	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]	Rooted			62.6706	61.8357	1.0135
	grb2-related adaptor protein. [swissprot;acc:q13588]	Measured		1	5986.65	6865.68	1.14683
	krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887]	Ranked			223.648	207.62	1.0772
	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	Squared	Subtracted	0	1.60583	1.26833	0.3375
	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	Measured		1	2353.63	3225.65	872.02
	protein cgi-147. [swissprot;acc:q9y3e5]	Ranked		0	5135.25	5298.12	162.87
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]			1	186.52	170.42	16.1
	scratch; scratch 1. [refseq;acc:nm_031309]		Divided	0	12164.9	12358.1	1.01588
	solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4]	Squared	Subtracted	1	26867.2	32335	5467.8
	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514]	Measured		0	599.896	604.911	5.015
	utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851]	Squared	Divided	1	29544.1	35678.3	1.20763
462	40s ribosomal protein s3. [swissprot;acc:p23396]	Rooted			50.6274	46.236	1.09498
	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	Ranked	Subtracted	0	10076.4	9928.08	148.32
	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]		Divided		12189.6	12378.3	1.01548
	dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325]	Squared			2400.71	2356.66	1.01869
	dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434]	Ranked	Subtracted	1	236.662	252.708	16.046
	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	Measured	Divided	0	11170.7	11305	1.01202
	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]	Squared	Subtracted		0.417515	0.742249	0.324734
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Rooted			6.9282	7.14143	0.21323
	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	Ranked	Divided	1	254.434	236.224	1.07709
	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4]	Rooted	Subtracted		49.0526	54.3781	5.3255
	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858]	Measured	Divided		11383.2	9926.61	1.14674
	s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991]		Subtracted		2353.63	3225.65	872.02
	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	Rooted	Divided	0	18.5298	18.2858	1.01334
	solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2]	Squared	Subtracted	1	26867.2	32335	5467.8
	survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637]	Measured		0	705.758	701.071	4.687
	ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350]	Squared	Divided	1	29540.4	35672.6	1.20759
463	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	Measured			3720.18	4264.46	1.1463
	calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194]	Squared			25533.3	30810.8	1.20669
	dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]	Measured		0	1262.65	1248.14	1.01163
	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	Ranked			5558.06	5473.99	1.01536
	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]	Squared			2403.2	2359.13	1.01868
	dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9]	Ranked		1	238.921	257.327	1.07704
	f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315]	Measured	Subtracted		2353.63	3225.65	872.02
	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	Ranked		0	11319.2	11463	143.8
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Rooted			6.9282	7.14143	0.21323
	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	Measured			146.622	150.709	4.087
	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	Rooted		1	68.8243	74.1496	5.3253
	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749]		Divided		50.2317	55.0025	1.09498
	secretory carrier-associated membrane protein 1. [swissprot;acc:o15126]	Squared	Subtracted		26866.1	32333.2	5467.1
	serpin b11. [swissprot;acc:q96p15]			0	0.417515	0.742249	0.324734
	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428]	Ranked		1	223.648	207.62	16.028
	transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724]	Rooted	Divided	0	35.7784	35.3221	1.01292
464	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	Measured	Subtracted		23	19	4
	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]	Rooted	Divided		30.3413	30.7252	1.01265
	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]	Ranked		1	210.578	226.764	1.07686

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.