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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Filtered description Value Type green Rank 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	green	Rank	red	network_comparison	
40s ribosomal protein s28. [source:swissprot;acc:p25112]	Squared	879.603	304	1054.58	1.19893	
40s ribosomal protein s28. [source:swissprot;acc:p25112]	Rooted	12.5026	285	13.5612	1.08467	
40s ribosomal protein s29. [source:swissprot;acc:p30054]	Measured	1895.38	297	1711.6	1.10737	
40s ribosomal protein s29. [source:swissprot;acc:p30054]	Ranked	9997.71	225	11035.3	1.10378	
40s ribosomal protein s29. [source:swissprot;acc:p30054]	Squared	6326.82	305	5295.67	1.19472	
40s ribosomal protein s29. [source:swissprot;acc:p30054]	Rooted	28.6733	265	26.1023	1.0985	
40s ribosomal protein s3a. [source:swissprot;acc:p49241]	Measured	2879.55	447	2929.51	1.01735	
40s ribosomal protein s3a. [source:swissprot;acc:p49241]	Ranked	10992.4	331	10405.1	1.05644	
40s ribosomal protein s3a. [source:swissprot;acc:p49241]	Squared	8550.86	473	8653.02	1.01195	
40s ribosomal protein s3a. [source:swissprot;acc:p49241]	Rooted	32.9781	404	34.0198	1.03159	
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	Measured	1495.22	255	1317.84	1.1346	
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	Ranked	11393.9	261	12448.9	1.09259	
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	Squared	5253.37	273	4224.07	1.24367	
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	Rooted	23.34	258	21.1334	1.10441	
40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	Measured	1495.66	254	1318.22	1.13461	
40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	Ranked	11392.6	260	12447.6	1.0926	
40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	Squared	5255.44	272	4225.7	1.24369	
40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	Rooted	23.3445	257	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	1104.61	315	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	12842.5	298	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	3141.67	411	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	19.8816	259	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	142.417	57	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	16053	288	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	15.1833	65	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	8.12243	83	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	808.929	287	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	8279.69	412	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	212.386	419	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	25.588	335	24.2756	1.05406	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	Measured	6739.34	313	6131.07	1.09921	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	Ranked	10560	233	9586.97	1.1015	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	Squared	54614.9	381	49458.1	1.10427	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	Rooted	47.6722	377	45.8794	1.03908	
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	Measured	1367.83	269	1217.92	1.12309	
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	Ranked	10545.7	199	11781.8	1.11721	
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	Squared	3102.4	262	2463.89	1.25915	
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	Rooted	24.6198	261	22.315	1.10328	
60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	Measured	1771.04	322	1621.1	1.09249	
60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	Ranked	9676.53	397	10006.9	1.03414	
60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	Squared	4339.96	259	3438.01	1.26235	
60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	Rooted	28.9062	355	27.6061	1.04709	
60s ribosomal protein l12 like protein. [source:sptrembl;acc:o60886]	Measured	1805.52	330	1658.23	1.08882	
60s ribosomal protein l12 like protein. [source:sptrembl;acc:o60886]	Ranked	9856.12	396	10194.8	1.03436	
60s ribosomal protein l12 like protein. [source:sptrembl;acc:o60886]	Squared	4640.77	265	3687.69	1.25845	
60s ribosomal protein l12 like protein. [source:sptrembl;acc:o60886]	Rooted	28.7604	362	27.5242	1.04491	
60s ribosomal protein l12. [source:swissprot;acc:p30050]	Measured	1805.05	328	1657.78	1.08884	
60s ribosomal protein l12. [source:swissprot;acc:p30050]	Ranked	9857.79	394	10196.9	1.0344	
60s ribosomal protein l12. [source:swissprot;acc:p30050]	Squared	4639.46	264	3686.65	1.25845	
60s ribosomal protein l12. [source:swissprot;acc:p30050]	Rooted	28.7547	360	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/