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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

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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 1332 to 1381 of 12912 in total

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

Rank	description	Value Type	red	green	network_comparison
333	nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]	Squared	14464.3	18142.8	1.25432
334	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793]		64975.9	81151.2	1.24894
	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Ranked	312	284	1.09859
	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669]	Rooted	58.6096	64.9655	1.10844
	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	17655.2	1.18298
335	40s ribosomal protein s11. [swissprot;acc:p04643]	Rooted	50.4705	45.5342	1.10841
	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Ranked	312	284	1.09859
	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	Measured	3494.31	4129.6	1.18181
	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	38253.3	1.24802
336	60s ribosomal protein l11. [swissprot;acc:p39026]	Rooted	50.3167	45.4063	1.10814
	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	284	1.09859
	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]	Measured	3751.3	4431.34	1.18128
	j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330]	Squared	46785.7	58383.2	1.24789
337	60s ribosomal protein l12. [swissprot;acc:p30050]	Ranked	243.583	267.527	1.0983
	carboxypeptidase b precursor. [refseq;acc:nm_020361]	Rooted	77.5801	70.0182	1.108
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Measured	20446.1	24136.4	1.18049
	human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503]	Squared	46785.7	58383.2	1.24789
338	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Ranked	243.583	267.528	1.0983
	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	Measured	20446.1	24136.4	1.18049
	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]	Rooted	77.58	70.0181	1.108
	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	58383.2	1.24789
339	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Ranked	243.583	267.527	1.0983
	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	Measured	20446.1	24136.4	1.18049
	human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629]	Squared	46785.7	58383.2	1.24789
	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	70.0179	1.108
340	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Measured	20446.1	24136.4	1.18049
	myelin gene expression factor 2. [refseq;acc:nm_016132]	Ranked	235.383	258.476	1.09811
	nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	Rooted	58.4926	64.8047	1.10791
	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	Squared	32117	40054	1.24713
341	60s ribosomal protein l9. [swissprot;acc:p32969]	Ranked	240.243	263.798	1.09805
	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	Measured	20446.1	24136.4	1.18049
	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	Rooted	51.9812	57.5858	1.10782
	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	Squared	32056.4	39965.8	1.24673
342	40s ribosomal protein s20. [swissprot;acc:p17075]	Ranked	243.5	267.21	1.09737
	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	Squared	70830.5	56822	1.24653
	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]	Measured	20446.1	24136.4	1.18049
	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848]	Rooted	49.2715	54.5757	1.10765
343	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]		50.3169	45.4333	1.10749
	conserved oligomeric golgi complex component 7. [swissprot;acc:p83436]	Squared	70830.5	56822	1.24653
	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	Measured	20446.1	24136.4	1.18049
	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	Ranked	241.625	265.136	1.0973
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	24136.4	1.18049
	isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735]	Squared	37226.9	46400.1	1.24641
	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55]	Rooted	49.4233	54.7327	1.10743
345	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143]		56.2615	62.2958	1.10725
	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	Measured	20446.1	24136.4	1.18049
	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961]	Squared	35793	44595.3	1.24592
	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]	Ranked	242.14	265.697	1.09729
346	40s ribosomal protein s3. [swissprot;acc:p23396]		241.612	265.119

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.