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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Filtered description Value Type Rank green Gene Interaction Map Network Comparison Type red network_comparison
Results: HTML CSV LaTeX Showing element 51 to 100 of 14920 in total 
Filtered	0
Interaction Map	High confidence
Network Comparison Type	Divided

description	Value Type	Rank	green	red	network_comparison	
40s ribosomal protein s28. [source:swissprot;acc:p25112]	Squared	304	879.603	1054.58	1.19893	
40s ribosomal protein s28. [source:swissprot;acc:p25112]	Rooted	285	12.5026	13.5612	1.08467	
40s ribosomal protein s29. [source:swissprot;acc:p30054]	Measured	297	1895.38	1711.6	1.10737	
40s ribosomal protein s29. [source:swissprot;acc:p30054]	Ranked	225	9997.71	11035.3	1.10378	
40s ribosomal protein s29. [source:swissprot;acc:p30054]	Squared	305	6326.82	5295.67	1.19472	
40s ribosomal protein s29. [source:swissprot;acc:p30054]	Rooted	265	28.6733	26.1023	1.0985	
40s ribosomal protein s3a. [source:swissprot;acc:p49241]	Measured	447	2879.55	2929.51	1.01735	
40s ribosomal protein s3a. [source:swissprot;acc:p49241]	Ranked	331	10992.4	10405.1	1.05644	
40s ribosomal protein s3a. [source:swissprot;acc:p49241]	Squared	473	8550.86	8653.02	1.01195	
40s ribosomal protein s3a. [source:swissprot;acc:p49241]	Rooted	404	32.9781	34.0198	1.03159	
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	Measured	255	1495.22	1317.84	1.1346	
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	Ranked	261	11393.9	12448.9	1.09259	
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	Squared	273	5253.37	4224.07	1.24367	
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	Rooted	258	23.34	21.1334	1.10441	
40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	Measured	254	1495.66	1318.22	1.13461	
40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	Ranked	260	11392.6	12447.6	1.0926	
40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	Squared	272	5255.44	4225.7	1.24369	
40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	Rooted	257	23.3445	21.1374	1.10442	
40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [source:swissprot;acc:p08865]	Measured	315	1104.61	1212.82	1.09796	
40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [source:swissprot;acc:p08865]	Ranked	298	12842.5	11977.8	1.07219	
40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [source:swissprot;acc:p08865]	Squared	411	3141.67	2967.63	1.05865	
40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [source:swissprot;acc:p08865]	Rooted	259	19.8816	21.9471	1.10389	
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [source:swissprot;acc:p17643]	Measured	57	142.417	270.264	1.89769	
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [source:swissprot;acc:p17643]	Ranked	288	16053	14930.6	1.07517	
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [source:swissprot;acc:p17643]	Squared	65	15.1833	50.642	3.33538	
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [source:swissprot;acc:p17643]	Rooted	83	8.12243	10.9038	1.34243	
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [source:swissprot;acc:p13196]	Measured	287	808.929	726.245	1.11385	
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [source:swissprot;acc:p13196]	Ranked	412	8279.69	8546.06	1.03217	
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [source:swissprot;acc:p13196]	Squared	419	212.386	202.436	1.04915	
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [source:swissprot;acc:p13196]	Rooted	335	25.588	24.2756	1.05406	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	Measured	313	6739.34	6131.07	1.09921	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	Ranked	233	10560	9586.97	1.1015	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	Squared	381	54614.9	49458.1	1.10427	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	Rooted	377	47.6722	45.8794	1.03908	
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	Measured	269	1367.83	1217.92	1.12309	
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	Ranked	199	10545.7	11781.8	1.11721	
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	Squared	262	3102.4	2463.89	1.25915	
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	Rooted	261	24.6198	22.315	1.10328	
60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	Measured	322	1771.04	1621.1	1.09249	
60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	Ranked	397	9676.53	10006.9	1.03414	
60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	Squared	259	4339.96	3438.01	1.26235	
60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	Rooted	355	28.9062	27.6061	1.04709	
60s ribosomal protein l12 like protein. [source:sptrembl;acc:o60886]	Measured	330	1805.52	1658.23	1.08882	
60s ribosomal protein l12 like protein. [source:sptrembl;acc:o60886]	Ranked	396	9856.12	10194.8	1.03436	
60s ribosomal protein l12 like protein. [source:sptrembl;acc:o60886]	Squared	265	4640.77	3687.69	1.25845	
60s ribosomal protein l12 like protein. [source:sptrembl;acc:o60886]	Rooted	362	28.7604	27.5242	1.04491	
60s ribosomal protein l12. [source:swissprot;acc:p30050]	Measured	328	1805.05	1657.78	1.08884	
60s ribosomal protein l12. [source:swissprot;acc:p30050]	Ranked	394	9857.79	10196.9	1.0344	
60s ribosomal protein l12. [source:swissprot;acc:p30050]	Squared	264	4639.46	3686.65	1.25845	
60s ribosomal protein l12. [source:swissprot;acc:p30050]	Rooted	360	28.7547	27.5183	1.04493	

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/