Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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

Results: HTML CSV LaTeX

Showing element 2660 to 2709 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
333	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	Ranked	1	312	284	1.09859
	nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	Measured		5039.63	5961.83	1.18299
	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4]	Rooted		49.0526	54.3781	1.10857
	nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]	Squared		14464.3	18142.8	1.25432
	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	Measured	0	634.305	584.237	1.0857
334	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793]	Squared	1	64975.9	81151.2	1.24894
	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	Rooted	0	10.603	10.0581	1.05418
	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]	Squared		3680.47	3222.63	1.14207
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	Ranked		8125.5	7697.5	1.0556
	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Ranked	1	312	284	1.09859
	peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521]	Measured	0	3161.12	2924.8	1.0808
	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669]	Rooted	1	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
	5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196]	Rooted	0	24.2756	25.588	1.05406
	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Ranked	1	312	284	1.09859
	germ cell-less. [refseq;acc:nm_022471]	Measured	0	1829.81	1694.05	1.08014
	keratin associated protein 1.5. [refseq;acc:nm_031957]	Squared		3680.43	3222.6	1.14207
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Ranked		8125.5	7697.5	1.0556
	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	Measured	1	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
	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Rooted	0	20.5317	19.4823	1.05386
	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	1	312	284	1.09859
	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	Measured	0	1766.66	1908.13	1.08008
	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]	Measured	1	3751.3	4431.34	1.18128
	j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330]	Squared	1	46785.7	58383.2	1.24789
	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]	Squared	0	3680.43	3222.6	1.14207
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	Ranked	0	8125.5	7697.5	1.0556
337	60s ribosomal protein l12. [swissprot;acc:p30050]	Ranked	1	243.583	267.527	1.0983
	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]	Measured	0	2039.07	2194.52	1.07624
	carboxypeptidase b precursor. [refseq;acc:nm_020361]	Rooted	1	77.5801	70.0182	1.108
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Rooted	0	56.92	59.965	1.0535
	glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210]	Ranked	0	12953.2	12273.2	1.05541
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Measured	1	20446.1	24136.4	1.18049
	human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503]	Squared	1	46785.7	58383.2	1.24789
	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]	Squared	0	3680.39	3222.57	1.14207
338	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Ranked	1	243.583	267.528	1.0983
	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	Measured	1	20446.1	24136.4	1.18049
	hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597]	Ranked	0	11149.7	10571.4	1.0547
	keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]	Squared		3680.31	3222.51	1.14206
	lamin b2. [swissprot;acc:q03252]	Measured		579.262	538.704	1.07529
	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]	Rooted	1	77.58	70.0181	1.108
	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	Rooted	0	9.92736	9.42407	1.0534
	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	1	46785.7	58383.2	1.24789
339	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Ranked	1	243.583	267.527	1.0983
	glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378]	Measured	0	996.883	1070.03	1.07338
	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]	Rooted	0	29.6274	31.1837	1.05253
	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	Measured	1	20446.1	24136.4	1.18049
	human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629]	Squared	1	46785.7	58383.2	1.24789

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.

- http://analysis.yellowcouch.org/