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 1301 to 1350 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
326	60s ribosomal protein l5. [source:swissprot;acc:p46777]	Ranked	241.899	265.924	1.09932	
326	anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [source:refseq;acc:nm_013366]	Squared	69124.3	54897.4	1.25915	
326	atp-dependent rna helicase ddx24 (dead-box protein 24). [source:swissprot;acc:q9gzr7]	Measured	3432.96	4081.21	1.18883	
326	ligatin (hepatocellular carcinoma-associated antigen 56). [source:swissprot;acc:p41214]	Rooted	50.3803	45.4193	1.10923	
327	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o43252]	Rooted	50.3803	45.4193	1.10923	
327	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [source:swissprot;acc:p24928]	Ranked	243.817	267.962	1.09903	
327	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	Squared	16424.1	20645.8	1.25704	
327	septin 10 isoform 1. [source:refseq;acc:nm_144710]	Measured	16067.4	19094.4	1.18839	
328	atp-dependent rna helicase ddx24 (dead-box protein 24). [source:swissprot;acc:q9gzr7]	Ranked	258.437	235.183	1.09888	
328	brain protein 44. [source:swissprot;acc:o95563]	Measured	15999.1	19007.1	1.18801	
328	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	Squared	16442.8	20662.7	1.25664	
328	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [source:swissprot;acc:p16435]	Rooted	50.3803	45.4193	1.10923	
329	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [source:swissprot;acc:q9y5k3]	Rooted	50.3803	45.4193	1.10923	
329	metaxin 2. [source:swissprot;acc:o75431]	Squared	41236	51807	1.25635	
329	neurogenic differentiation factor 2 (neurod2). [source:swissprot;acc:q15784]	Ranked	312	284	1.09859	
329	septin 7 (cdc10 protein homolog). [source:swissprot;acc:q16181]	Measured	15999.1	19007.1	1.18801	
330	60s ribosomal protein l32. [source:swissprot;acc:p02433]	Rooted	50.519	45.5497	1.1091	
330	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [source:swissprot;acc:q12873]	Ranked	312	284	1.09859	
330	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	Squared	16203.4	20339.9	1.25529	
330	septin 6. [source:swissprot;acc:q14141]	Measured	15959.9	18957.1	1.1878	
331	apical-like protein (apxl protein). [source:swissprot;acc:q13796]	Rooted	60.6697	67.2802	1.10896	
331	doc-1 related protein (doc-1r). [source:swissprot;acc:o75956]	Ranked	312	284	1.09859	
331	pre-mrna cleavage complex ii protein pcf11 (fragment). [source:swissprot;acc:o94913]	Measured	20287.2	17083.8	1.18751	
331	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [source:swissprot;acc:p31350]	Squared	33100.3	41520.6	1.25439	
332	neurogenic differentiation factor 6 (neurod6) (my051 protein). [source:swissprot;acc:q96nk8]	Ranked	312	284	1.09859	
332	nucleotide-binding protein 1 (nbp 1). [source:swissprot;acc:p53384]	Squared	14464.3	18142.8	1.25432	
332	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [source:refseq;acc:nm_002669]	Measured	5051.16	5975.51	1.183	
332	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [source:refseq;acc:nm_020859]	Rooted	60.6732	67.2827	1.10894	
333	neurogenic differentiation factor 1 (neurod1) (neurod). [source:swissprot;acc:q13562]	Ranked	312	284	1.09859	
333	nuclear matrix protein nmp200 related to splicing factor prp19. [source:refseq;acc:nm_014502]	Measured	5039.63	5961.83	1.18299	
333	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [source:swissprot;acc:q9bze4]	Rooted	49.0526	54.3781	1.10857	
333	nucleotide binding protein 2 (nbp 2). [source:swissprot;acc:q9y5y2]	Squared	14464.3	18142.8	1.25432	
334	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [source:refseq;acc:nm_138793]	Squared	64975.9	81151.2	1.24894	
334	neurogenic differentiation factor 4 (neurod4). [source:swissprot;acc:q9hd90]	Ranked	312	284	1.09859	
334	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [source:refseq;acc:nm_002669]	Rooted	58.6096	64.9655	1.10844	
334	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). [source:swissprot;acc:o43236]	Measured	14924.4	17655.2	1.18298	
335	40s ribosomal protein s11. [source:swissprot;acc:p04643]	Rooted	50.4705	45.5342	1.10841	
335	chromodomain helicase dna binding protein 5. [source:refseq;acc:nm_015557]	Ranked	312	284	1.09859	
335	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [source:swissprot;acc:q9ny93]	Measured	3494.31	4129.6	1.18181	
335	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [source:refseq;acc:nm_016304]	Squared	30651.3	38253.3	1.24802	
336	60s ribosomal protein l11. [source:swissprot;acc:p39026]	Rooted	50.3167	45.4063	1.10814	
336	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [source:swissprot;acc:o14519]	Ranked	312	284	1.09859	
336	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [source:swissprot;acc:q9nr33]	Measured	3751.3	4431.34	1.18128	
336	j kappa-recombination signal binding protein (rbp-j kappa). [source:swissprot;acc:q06330]	Squared	46785.7	58383.2	1.24789	
337	60s ribosomal protein l12. [source:swissprot;acc:p30050]	Ranked	243.583	267.527	1.0983	
337	carboxypeptidase b precursor. [source:refseq;acc:nm_020361]	Rooted	77.5801	70.0182	1.108	
337	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Measured	20446.1	24136.4	1.18049	
337	human immunodeficiency virus type i enhancer binding protein 3. [source:refseq;acc:nm_024503]	Squared	46785.7	58383.2	1.24789	
338	60s ribosomal protein l12 like protein. [source:sptrembl;acc:o60886]	Ranked	243.583	267.528	1.0983	
338	homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]	Measured	20446.1	24136.4	1.18049	

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/