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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 880 to 929 of 3730 in total

Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	Filtered	red	green	network_comparison	
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	
454	transducin-like enhancer protein 1 (esg1). [source:swissprot;acc:q04724]	0	3219.3	3174.79	1.01402	
455	ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [source:swissprot;acc:q06546]	1	4890.51	5610.95	1.14731	
455	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [source:refseq;acc:nm_030949]	0	2403.53	2371.24	1.01362	
456	cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [source:swissprot;acc:q13098]	0	17356	17126	1.01343	
456	ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [source:swissprot;acc:q06545]	1	4890.51	5610.95	1.14731	
457	dna mismatch repair protein mlh1 (mutl protein homolog 1). [source:swissprot;acc:p40692]	0	1562.36	1541.69	1.01341	
457	nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [source:swissprot;acc:o00217]	1	4890.51	5610.95	1.14731	
458	elongation of very long chain fatty acids protein 1 (cgi-88). [source:swissprot;acc:q9bw60]	1	4890.55	5610.96	1.14731	
458	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [source:swissprot;acc:q9h1b4]	0	2633.61	2668.56	1.01327	
459	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [source:swissprot;acc:q15811]	0	3774.08	3821.87	1.01266	
459	myc proto-oncogene protein (c-myc). [source:swissprot;acc:p01106]	1	4892.16	5611.48	1.14704	
460	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [source:swissprot;acc:q9nzm3]	0	3693.07	3739.55	1.01259	
460	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [source:swissprot;acc:p56182]	1	3790.11	4346.98	1.14693	
461	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [source:swissprot;acc:q9y2s0]	0	1915.69	1892.44	1.01229	
461	grb2-related adaptor protein. [source:swissprot;acc:q13588]	1	5986.65	6865.68	1.14683	
462	leucine rich repeat (in flii) interacting protein 1. [source:refseq;acc:nm_004735]	0	11170.7	11305	1.01202	
462	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [source:swissprot;acc:o60858]	1	11383.2	9926.61	1.14674	
463	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [source:swissprot;acc:q9nvp1]	1	3720.18	4264.46	1.1463	
463	dihydrofolate reductase (ec 1.5.1.3). [source:swissprot;acc:p00374]	0	1262.65	1248.14	1.01163	
464	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [source:swissprot;acc:q16576]	1	4858.96	5568.85	1.1461	
464	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [source:swissprot;acc:o43708]	0	2290.09	2264.37	1.01136	
465	homer, neuronal immediate early gene, 1b. [source:refseq;acc:nm_004272]	0	6323	6254.09	1.01102	

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/