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	network_comparison	green

Results: HTML CSV LaTeX

Showing element 1325 to 1374 of 12912 in total

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

Rank	description	Value Type	red	network_comparison	green
332	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	Ranked	312	1.09859	284
	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	Squared	14464.3	1.25432	18142.8
	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669]	Measured	5051.16	1.183	5975.51
	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	Rooted	60.6732	1.10894	67.2827
333	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	Ranked	312	1.09859	284
	nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	Measured	5039.63	1.18299	5961.83
	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4]	Rooted	49.0526	1.10857	54.3781
	nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]	Squared	14464.3	1.25432	18142.8
334	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793]		64975.9	1.24894	81151.2
	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Ranked	312	1.09859	284
	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669]	Rooted	58.6096	1.10844	64.9655
	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236]	Measured	14924.4	1.18298	17655.2
335	40s ribosomal protein s11. [swissprot;acc:p04643]	Rooted	50.4705	1.10841	45.5342
	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Ranked	312	1.09859	284
	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	Measured	3494.31	1.18181	4129.6
	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304]	Squared	30651.3	1.24802	38253.3
336	60s ribosomal protein l11. [swissprot;acc:p39026]	Rooted	50.3167	1.10814	45.4063
	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]	Ranked	312	1.09859	284
	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]	Measured	3751.3	1.18128	4431.34
	j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330]	Squared	46785.7	1.24789	58383.2
337	60s ribosomal protein l12. [swissprot;acc:p30050]	Ranked	243.583	1.0983	267.527
	carboxypeptidase b precursor. [refseq;acc:nm_020361]	Rooted	77.5801	1.108	70.0182
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Measured	20446.1	1.18049	24136.4
	human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503]	Squared	46785.7	1.24789	58383.2
338	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Ranked	243.583	1.0983	267.528
	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	Measured	20446.1	1.18049	24136.4
	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]	Rooted	77.58	1.108	70.0181
	zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822]	Squared	46785.7	1.24789	58383.2
339	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Ranked	243.583	1.0983	267.527
	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	Measured	20446.1	1.18049	24136.4
	human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629]	Squared	46785.7	1.24789	58383.2
	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872]	Rooted	77.5797	1.108	70.0179
340	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Measured	20446.1	1.18049	24136.4
	myelin gene expression factor 2. [refseq;acc:nm_016132]	Ranked	235.383	1.09811	258.476
	nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	Rooted	58.4926	1.10791	64.8047
	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	Squared	32117	1.24713	40054
341	60s ribosomal protein l9. [swissprot;acc:p32969]	Ranked	240.243	1.09805	263.798
	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	Measured	20446.1	1.18049	24136.4
	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	Rooted	51.9812	1.10782	57.5858
	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	Squared	32056.4	1.24673	39965.8
342	40s ribosomal protein s20. [swissprot;acc:p17075]	Ranked	243.5	1.09737	267.21
	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	Squared	70830.5	1.24653	56822
	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]	Measured	20446.1	1.18049	24136.4
	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848]	Rooted	49.2715	1.10765	54.5757
343	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]		50.3169	1.10749	45.4333
	conserved oligomeric golgi complex component 7. [swissprot;acc:p83436]	Squared	70830.5	1.24653	56822
	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	Measured	20446.1	1.18049	24136.4
	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	Ranked	241.625	1.0973	265.136
344	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Measured	20446.1	1.18049	24136.4

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.