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 2908 to 2957 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison
364	dok-like protein. [refseq;acc:nm_024872]	Measured	Subtracted	6102.59	7081.46	978.87
	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]		Divided	5189	6088.47	1.17334
	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	Rooted	Subtracted	60.594	67.2244	6.6304
	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	Squared	Divided	17957.2	22234.1	1.23817
	small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173]		Subtracted	34068.1	40330.8	6262.7
365	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	Ranked	Divided	242.744	266.07	1.09609
	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	Squared		17965.8	22243	1.23807
	calcyphosine. [swissprot;acc:q13938]	Measured		5189	6088.47	1.17334
	di-ras2. [refseq;acc:nm_017594]	Squared	Subtracted	34068	40330.7	6262.7
	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]	Measured		6102.59	7081.46	978.87
	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	Ranked		233.539	253.197	19.658
	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	Rooted	Divided	49.7541	54.9425	1.10428
	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]		Subtracted	63.0715	56.4506	6.6209
366	40s ribosomal protein s15a. [swissprot;acc:p39027]		Divided	50.5463	45.7763	1.1042
	40s ribosomal protein s5. [swissprot;acc:p46782]	Ranked		242.473	265.756	1.09602
	apical-like protein (apxl protein). [swissprot;acc:q13796]	Rooted	Subtracted	60.6697	67.2802	6.6105
	ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	Squared	Divided	62783.5	50784.1	1.23628
	cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155]	Ranked	Subtracted	233.539	253.197	19.658
	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	Measured	Divided	5189	6088.47	1.17334
	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]		Subtracted	6102.59	7081.46	978.87
	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497]	Squared		29101.9	35347	6245.1
367	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	Rooted	Divided	49.0882	54.2027	1.10419
	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414]	Squared		62757.7	50767.8	1.23617
	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159]	Ranked	Subtracted	218.827	238.407	19.58
	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864]	Measured	Divided	4024.4	4719.35	1.17268
	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	Ranked		234.146	256.627	1.09601
	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]	Squared	Subtracted	29101.9	35347	6245.1
	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	Rooted		60.6732	67.2827	6.6095
	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685]	Measured		6102.59	7081.46	978.87
368	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]	Squared		29098.8	35342.6	6243.8
	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	Ranked		218.827	238.407	19.58
	dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442]	Squared	Divided	51805.2	41916.4	1.23592
	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	Rooted	Subtracted	63.0663	56.4667	6.5996
	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]		Divided	49.5225	54.6817	1.10418
	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	Measured		5082.66	5959.99	1.17261
	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361]		Subtracted	7756.51	8731.76	975.25
	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	Ranked	Divided	242.66	265.715	1.09501
369	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]			242.159	265.104	1.09475
	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	Measured		3583.56	4194.95	1.17061
	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388]	Ranked	Subtracted	239.977	259.525	19.548
	galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182]	Squared	Divided	45960.8	56749.6	1.23474
	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]	Rooted		49.7435	45.0586	1.10397
	nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531]	Measured	Subtracted	7755.69	8730.74	975.05
	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]	Rooted		63.0663	56.4667	6.5996
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Squared		29096	35338.7	6242.7
370	grancalcin. [swissprot;acc:p28676]			29095.7	35338.3	6242.6
	grb2-related adaptor protein. [swissprot;acc:q13588]	Rooted		61.4282	68.0107	6.5825
	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	Measured	Divided	4108.15	4808.93	1.17058
	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579]	Rooted		49.7435	45.0586	1.10397
	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	Ranked	Subtracted	218.818	238.358	19.54

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.