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 858 to 907 of 3730 in total

Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	Filtered	red	green	network_comparison	
429	vinexin (sh3-containing adaptor molecule-1) (scam-1). [source:swissprot;acc:o60504]	1	6272.91	7226.06	1.15195	
430	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [source:swissprot;acc:p31040]	0	10247.8	10535	1.02803	
430	transcription factor dp-2 (e2f dimerization partner 2). [source:swissprot;acc:q14188]	1	3804.09	4379.37	1.15123	
431	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [source:refseq;acc:nm_022779]	1	3849.94	4431.36	1.15102	
431	nascent-polypeptide-associated complex alpha polypeptide. [source:refseq;acc:nm_005594]	0	146.622	150.709	1.02787	
432	high-glucose-regulated protein 8 (ny-ren-2 antigen). [source:swissprot;acc:q9y5a9]	0	100.5	103.25	1.02736	
432	mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [source:swissprot;acc:o75439]	1	5244.71	6036.27	1.15093	
433	mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [source:swissprot;acc:q10713]	1	5244.88	6036.38	1.15091	
433	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). [source:swissprot;acc:q9nzq3]	0	100.5	103.25	1.02736	
434	testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [source:swissprot;acc:p16562]	0	201	206.5	1.02736	
434	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [source:swissprot;acc:p31930]	1	5246.38	6037.37	1.15077	
435	elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [source:swissprot;acc:q14576]	0	5891.28	5737.71	1.02677	
435	proline synthetase co-transcribed bacterial homolog protein. [source:swissprot;acc:o94903]	1	5233.86	6022.6	1.1507	
436	alpha-nac protein. [source:sptrembl;acc:q9h009]	0	147.221	151.122	1.0265	
436	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [source:refseq;acc:nm_021069]	1	6230.94	7168.2	1.15042	
437	protein cgi-140 (protein ptd008) (my006 protein). [source:swissprot;acc:q9y284]	0	2331	2390	1.02531	
437	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [source:swissprot;acc:q9nq55]	1	3779.92	4348.48	1.15042	
438	3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	0	2925.57	2853.65	1.0252	
438	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [source:swissprot;acc:o14497]	1	6252.58	7192.88	1.15039	
439	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [source:swissprot;acc:o75340]	1	6252.58	7192.88	1.15039	
439	protein c20orf45 (cgi-107). [source:swissprot;acc:q9y3b1]	0	532.667	546	1.02503	
440	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [source:swissprot;acc:p04632]	1	6251.91	7192.08	1.15038	
440	limbic system-associated membrane protein precursor (lsamp). [source:swissprot;acc:q13449]	0	6830.67	7000.85	1.02491	
441	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [source:refseq;acc:nm_032468]	0	6158	6303	1.02355	
441	grancalcin. [source:swissprot;acc:p28676]	1	6251.96	7192.13	1.15038	
442	repressor of estrogen receptor activity; b-cell associated protein. [source:refseq;acc:nm_007273]	0	6699.82	6856.28	1.02335	
442	sorcin (22 kda protein) (cp-22) (v19). [source:swissprot;acc:p30626]	1	6251.99	7192.17	1.15038	
443	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [source:refseq;acc:nm_020732]	1	6252.27	7192.51	1.15038	
443	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [source:refseq;acc:nm_015920]	0	2432.41	2379.52	1.02223	
444	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [source:swissprot;acc:p42677]	0	2431.87	2378.99	1.02223	
444	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [source:swissprot;acc:q99848]	1	3758.67	4322.87	1.15011	
445	ad24 protein. [source:refseq;acc:nm_022451]	1	3753.71	4315.95	1.14978	
445	mstp028 protein. [source:refseq;acc:nm_031954]	0	9988.45	9808.48	1.01835	
446	mevalonate kinase (ec 2.7.1.36) (mk). [source:swissprot;acc:q03426]	0	1549.26	1522.06	1.01787	
446	nucleostemin; putative nucleotide binding protein, estradiol-induced. [source:refseq;acc:nm_014366]	1	3766.03	4329.37	1.14958	
447	40s ribosomal protein s3a. [source:swissprot;acc:p49241]	0	2929.51	2879.55	1.01735	
447	pescadillo homolog 1. [source:swissprot;acc:o00541]	1	3751.14	4310.89	1.14922	
448	ponsin; sh3-domain protein 5 (ponsin). [source:refseq;acc:nm_015385]	1	6259.3	7190.91	1.14884	
448	protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [source:swissprot;acc:p07237]	0	524.415	533.236	1.01682	
449	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [source:swissprot;acc:o14640]	0	5699.32	5607.7	1.01634	
449	wd-repeat protein 12 (ytm1 homolog). [source:swissprot;acc:q9gzl7]	1	3761.59	4319.69	1.14837	
450	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [source:sptrembl;acc:q9ujn8]	0	4158.33	4094.09	1.01569	
450	l-myc-1 proto-oncogene protein. [source:swissprot;acc:p12524]	1	4889.21	5610.52	1.14753	
451	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	0	2683.61	2642.79	1.01545	
451	n-myc proto-oncogene protein. [source:swissprot;acc:p04198]	1	4889.71	5610.69	1.14745	
452	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [source:swissprot;acc:p24298]	0	1527.36	1504.85	1.01496	
452	zinc finger-like protein 9. [source:refseq;acc:nm_033414]	1	3760.8	4315.06	1.14738	
453	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [source:swissprot;acc:p54132]	0	1337.29	1356.52	1.01438	
453	membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [source:swissprot;acc:q9umx9]	1	3760.8	4315.06	1.14738	
454	guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [source:swissprot;acc:p36915]	1	3760.8	4315.06	1.14738	

Legend:
- Rank is the rank after comparing the two networks
- 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/