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 3508 to 3557 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
439	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]	Squared	0	9.26264	9.58152	1.03443
	histone h2b. [refseq;acc:nm_175055]	Ranked		8770.3	8574.79	1.0228
	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]	Rooted		23.2671	22.7187	1.02414
	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]	Measured	1	6252.58	7192.88	1.15039
	protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1]		0	532.667	546	1.02503
440	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632]		1	6251.91	7192.08	1.15038
	dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388]	Squared		26348.4	31925.8	1.21168
	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]	Rooted		63.2134	69.352	1.09711
	highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101]	Ranked		231.802	249.983	1.07843
	histone h2b.e (h2b/e). [swissprot;acc:q99879]	Ranked	0	8770.28	8574.81	1.0228
	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	Squared		9.26264	9.58152	1.03443
	limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449]	Measured		6830.67	7000.85	1.02491
	similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9]	Rooted		22.7692	22.2374	1.02391
441	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]	Measured		6158	6303	1.02355
	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	Rooted		19.9002	19.441	1.02362
	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	Squared	1	26348.7	31924.3	1.21161
	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]	Rooted		63.2134	69.352	1.09711
	grancalcin. [swissprot;acc:p28676]	Measured		6251.96	7192.13	1.15038
	grb2-related adaptor protein. [swissprot;acc:q13588]	Ranked		223.457	207.222	1.07835
	histone h2b.c (h2b/c). [swissprot;acc:q99880]	Ranked	0	8770.14	8574.98	1.02276
	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]	Squared	0	25552.2	26410.4	1.03359
442	centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451]	Squared	1	51286.6	42334.5	1.21146
	e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140]	Ranked	1	223.802	207.55	1.0783
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Ranked	0	14570.4	14247.3	1.02268
	kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8]	Rooted		29.7464	29.0619	1.02355
	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	Squared		18476.6	19091.9	1.0333
	repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]	Measured		6699.82	6856.28	1.02335
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Measured	1	6251.99	7192.17	1.15038
	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685]	Rooted		63.2134	69.352	1.09711
443	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	Rooted		50.1766	45.7369	1.09707
	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]	Measured		6252.27	7192.51	1.15038
	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	Rooted	0	19.3683	19.8189	1.02326
	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]	Squared	0	26171.8	27038.8	1.03313
	neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117]	Ranked	1	223.79	207.539	1.0783
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Ranked	0	9141.6	8940.14	1.02253
	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920]	Measured	0	2432.41	2379.52	1.02223
	translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199]	Squared	1	26472.8	32067.7	1.21135
444	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]	Measured	0	2431.87	2378.99	1.02223
	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	Rooted	1	50.1636	45.7275	1.09701
	alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652]	Squared	0	3778.75	3670.49	1.02949
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Ranked		14556.7	14237.8	1.0224
	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	Rooted		42.0329	43.0082	1.0232
	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443]	Ranked	1	223.801	207.549	1.0783
	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848]	Measured		3758.67	4322.87	1.15011
	ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965]	Squared		58831	48584.2	1.21091
445	ad24 protein. [refseq;acc:nm_022451]	Measured		3753.71	4315.95	1.14978
	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]	Rooted	0	42.0329	43.0082	1.0232
	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	Ranked		7965.06	7790.78	1.02237
	mstp028 protein. [refseq;acc:nm_031954]	Measured		9988.45	9808.48	1.01835
	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903]	Ranked	1	223.801	207.549	1.0783

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/