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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 4658 to 4707 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
292	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	Measured	Divided	0	11223	12473	1.11138
	crk-like protein. [swissprot;acc:p46109]	Squared	Subtracted	1	28896.2	36767	7870.8
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Ranked		0	11959.8	12731.1	771.3
	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]			1	234.146	256.627	22.481
	neuralized-like. [refseq;acc:nm_004210]	Squared	Divided		6828.26	8728.66	1.27831
	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	Measured			4641.09	5588.75	1.20419
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]		Subtracted		950.561	2108.52	1157.96
	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	Rooted			66.1064	74.1074	8.001
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	Ranked	Divided	0	10280.5	9574.98	1.07368
	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920]	Squared	Subtracted		6607.52	6525.61	81.91
	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	Measured			952.488	863.886	88.602
	sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]	Rooted			5.01247	6.80523	1.79276
	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	Squared	Divided		7073.9	8609.96	1.21714
	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]	Rooted			56.49	52.4119	1.07781
	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]			1	56.48	63.119	1.11755
293	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]	Squared	Subtracted	0	6605.9	6524	81.9
	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	Ranked	Divided	1	240.782	265.717	1.10356
	adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123]	Measured	Subtracted	0	764.479	676.971	87.508
	block 23. [sptrembl;acc:q8nhw5]		Divided		1943.32	2159.55	1.11127
	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5]	Ranked	Subtracted	1	219.421	196.978	22.443
	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	Squared	Divided	0	30195	24837.5	1.2157
	ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]	Rooted	Subtracted		24.6278	26.4005	1.7727
	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]	Squared	Divided	1	35991.8	46002.9	1.27815
	mesoderm induction early response 1. [refseq;acc:nm_020948]	Rooted		0	43.1585	40.0869	1.07662
	nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]	Measured		1	4641.09	5588.75	1.20419
	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519]	Squared	Subtracted		28896.2	36767	7870.8
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	Ranked	Divided	0	10287.1	9583.27	1.07344
	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]		Subtracted		12121.6	12887.6	766
	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	Rooted	Divided	1	63.0715	56.4506	1.11729
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Measured	Subtracted		4512.19	5655.52	1143.33
	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631]	Rooted			66.1064	74.1074	8.001
294	1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120]	Squared	Divided		30826.5	39383.9	1.2776
	brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567]	Ranked			240.782	265.717	1.10356
	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	Measured			22515.5	18702.6	1.20387
	crk-like protein. [swissprot;acc:p46109]	Rooted	Subtracted		66.1064	74.1074	8.001
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Ranked		0	11935.6	12698.9	763.3
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]			1	219.421	196.978	22.443
	kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8]	Squared	Divided	0	290.82	239.342	1.21508
	lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776]	Measured	Subtracted		841.301	753.849	87.452
	mesoderm induction early response 1. [refseq;acc:nm_020948]		Divided		1914.5	1723.5	1.11082
	nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718]	Squared	Subtracted		16.747	98.4675	81.7205
	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241]			1	28896.2	36767	7870.8
	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Rooted	Divided		59.0296	65.951	1.11725
	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]	Measured	Subtracted		4512.19	5655.52	1143.33
	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514]	Ranked	Divided	0	13981.5	13025.1	1.07343
	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]	Rooted	Subtracted		39.7617	37.9899	1.7718
	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695]		Divided		35.7516	38.4588	1.07572
295	1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943]	Squared		1	30807.7	39351.7	1.27733
	adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5]	Measured		0	426.8	384.843	1.10902
	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]		Subtracted	1	5720.25	4577.5	1142.75

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.