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 686 to 735 of 3730 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	Filtered	red	green	network_comparison	
343	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [source:swissprot;acc:o60678]	1	241.625	265.136	1.0973	
344	40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	1	241.625	265.136	1.0973	
344	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [source:swissprot;acc:q12882]	0	10540.6	10027.6	1.05116	
345	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [source:swissprot;acc:p11766]	0	11563.7	12151.8	1.05086	
345	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [source:swissprot;acc:p30085]	1	242.14	265.697	1.09729	
346	40s ribosomal protein s3. [source:swissprot;acc:p23396]	1	241.612	265.119	1.09729	
346	rna polymerase i transcription factor rrn3. [source:refseq;acc:nm_018427]	0	9267.81	9736.2	1.05054	
347	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [source:swissprot;acc:p16870]	0	7670	7311	1.0491	
347	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [source:swissprot;acc:q9uij7]	1	242.14	265.697	1.09729	
348	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p27144]	1	242.14	265.696	1.09728	
348	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [source:refseq;acc:nm_030801]	0	16321	15577	1.04776	
349	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [source:swissprot;acc:p43357]	0	16321	15577	1.04776	
349	surfeit locus protein 5. [source:swissprot;acc:q15528]	1	242.14	265.696	1.09728	
350	melanoma-associated antigen 11 (mage-11 antigen). [source:swissprot;acc:p43364]	0	16321	15577	1.04776	
350	zinc finger protein 291. [source:swissprot;acc:q9by12]	1	242.14	265.696	1.09728	
351	melanoma-associated antigen 2 (mage-2 antigen). [source:swissprot;acc:p43356]	0	16321	15577	1.04776	
351	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [source:swissprot;acc:o43933]	1	242.14	265.696	1.09728	
352	hepatocellular carcinoma-associated protein hca1. [source:refseq;acc:nm_020932]	0	16321	15577	1.04776	
352	protein 1-4 (atp binding protein associated with cell differentiation). [source:swissprot;acc:o14530]	1	242.14	265.696	1.09728	
353	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [source:swissprot;acc:p43360]	0	16321	15577	1.04776	
353	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [source:swissprot;acc:o14908]	1	231.73	211.252	1.09694	
354	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [source:swissprot;acc:q9y5v3]	0	16321	15577	1.04776	
354	syntaxin 10 (syn10). [source:swissprot;acc:o60499]	1	234.691	257.442	1.09694	
355	melanoma-associated antigen f1 (mage-f1 antigen). [source:swissprot;acc:q9hay2]	0	16321	15577	1.04776	
355	syntaxin 6. [source:swissprot;acc:o43752]	1	234.673	257.414	1.09691	
356	60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	1	243.24	266.796	1.09684	
356	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [source:swissprot;acc:p43358]	0	16321	15577	1.04776	
357	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	1	243.12	266.661	1.09683	
357	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	0	16321	15577	1.04776	
358	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	0	16321	15577	1.04776	
358	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	1	243.12	266.662	1.09683	
359	60s ribosomal protein l4 (l1). [source:swissprot;acc:p36578]	1	239.277	262.434	1.09678	
359	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	0	16321	15577	1.04776	
360	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]	0	16321	15577	1.04776	
360	protein transport protein sec61 gamma subunit. [source:swissprot;acc:p38384]	1	243.072	266.559	1.09663	
361	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [source:swissprot;acc:p43355]	0	16321	15577	1.04776	
361	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [source:refseq;acc:nm_022061]	1	242.83	266.248	1.09644	
362	apical-like protein (apxl protein). [source:swissprot;acc:q13796]	1	231.492	211.136	1.09641	
362	melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]	0	16321	15577	1.04776	
363	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [source:swissprot;acc:p43366]	0	16321	15577	1.04776	
363	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [source:refseq;acc:nm_020859]	1	231.481	211.131	1.09639	
364	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [source:swissprot;acc:p30876]	1	243.208	266.617	1.09625	
364	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [source:swissprot;acc:q9unf1]	0	16321	15577	1.04776	
365	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [source:swissprot;acc:q9p0j6]	1	242.744	266.07	1.09609	
365	transcription factor e2f2 (e2f-2). [source:swissprot;acc:q14209]	0	7769.96	8139.71	1.04759	
366	40s ribosomal protein s5. [source:swissprot;acc:p46782]	1	242.473	265.756	1.09602	
366	glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [source:swissprot;acc:p23378]	0	8614.89	9017.27	1.04671	
367	f-actin capping protein alpha-2 subunit (capz alpha-2). [source:swissprot;acc:p47755]	0	13801.7	13185.9	1.0467	
367	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [source:swissprot;acc:p52272]	1	234.146	256.627	1.09601	
368	adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [source:swissprot;acc:p56377]	0	16679.2	15940.6	1.04633	

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/