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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Gene Rank description Value Type Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 330 to 379 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	green	red	network_comparison	
330	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [source:swissprot;acc:q12873]	284	312	1.09859	
331	doc-1 related protein (doc-1r). [source:swissprot;acc:o75956]	284	312	1.09859	
332	neurogenic differentiation factor 6 (neurod6) (my051 protein). [source:swissprot;acc:q96nk8]	284	312	1.09859	
333	neurogenic differentiation factor 1 (neurod1) (neurod). [source:swissprot;acc:q13562]	284	312	1.09859	
334	neurogenic differentiation factor 4 (neurod4). [source:swissprot;acc:q9hd90]	284	312	1.09859	
335	chromodomain helicase dna binding protein 5. [source:refseq;acc:nm_015557]	284	312	1.09859	
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]	284	312	1.09859	
337	60s ribosomal protein l12. [source:swissprot;acc:p30050]	267.527	243.583	1.0983	
338	60s ribosomal protein l12 like protein. [source:sptrembl;acc:o60886]	267.528	243.583	1.0983	
339	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [source:sptrembl;acc:q9nq02]	267.527	243.583	1.0983	
340	myelin gene expression factor 2. [source:refseq;acc:nm_016132]	258.476	235.383	1.09811	
341	60s ribosomal protein l9. [source:swissprot;acc:p32969]	263.798	240.243	1.09805	
342	40s ribosomal protein s20. [source:swissprot;acc:p17075]	267.21	243.5	1.09737	
343	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [source:swissprot;acc:o60678]	265.136	241.625	1.0973	
344	40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	265.136	241.625	1.0973	
345	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [source:swissprot;acc:p30085]	265.697	242.14	1.09729	
346	40s ribosomal protein s3. [source:swissprot;acc:p23396]	265.119	241.612	1.09729	
347	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [source:swissprot;acc:q9uij7]	265.697	242.14	1.09729	
348	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p27144]	265.696	242.14	1.09728	
349	surfeit locus protein 5. [source:swissprot;acc:q15528]	265.696	242.14	1.09728	
350	zinc finger protein 291. [source:swissprot;acc:q9by12]	265.696	242.14	1.09728	
351	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [source:swissprot;acc:o43933]	265.696	242.14	1.09728	
352	protein 1-4 (atp binding protein associated with cell differentiation). [source:swissprot;acc:o14530]	265.696	242.14	1.09728	
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]	211.252	231.73	1.09694	
354	syntaxin 10 (syn10). [source:swissprot;acc:o60499]	257.442	234.691	1.09694	
355	syntaxin 6. [source:swissprot;acc:o43752]	257.414	234.673	1.09691	
356	60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	266.796	243.24	1.09684	
357	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	266.661	243.12	1.09683	
358	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	266.662	243.12	1.09683	
359	60s ribosomal protein l4 (l1). [source:swissprot;acc:p36578]	262.434	239.277	1.09678	
360	protein transport protein sec61 gamma subunit. [source:swissprot;acc:p38384]	266.559	243.072	1.09663	
361	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [source:refseq;acc:nm_022061]	266.248	242.83	1.09644	
362	apical-like protein (apxl protein). [source:swissprot;acc:q13796]	211.136	231.492	1.09641	
363	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [source:refseq;acc:nm_020859]	211.131	231.481	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]	266.617	243.208	1.09625	
365	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [source:swissprot;acc:q9p0j6]	266.07	242.744	1.09609	
366	40s ribosomal protein s5. [source:swissprot;acc:p46782]	265.756	242.473	1.09602	
367	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [source:swissprot;acc:p52272]	256.627	234.146	1.09601	
368	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [source:swissprot;acc:q9y606]	265.715	242.66	1.09501	
369	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [source:swissprot;acc:p52815]	265.104	242.159	1.09475	
370	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [source:refseq;acc:nm_031438]	265.104	242.159	1.09475	
371	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [source:refseq;acc:nm_012424]	170.42	186.52	1.09447	
372	ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	170.42	186.52	1.09447	
373	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [source:swissprot;acc:q9y3b7]	265.255	242.37	1.09442	
374	transcription factor dp-2 (e2f dimerization partner 2). [source:swissprot;acc:q14188]	244.168	267.208	1.09436	
375	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [source:swissprot;acc:o14802]	265.516	242.686	1.09407	
376	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [source:swissprot;acc:q9ny93]	234.945	257.017	1.09395	
377	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [source:swissprot;acc:o95602]	265.481	242.691	1.09391	
378	60s ribosomal protein l30. [source:swissprot;acc:p04645]	265.365	242.593	1.09387	
379	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p54819]	264.163	241.509	1.0938	

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/