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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 343 to 392 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
343	homeobox protein hox-a5 (hox-1c). [source:swissprot;acc:p20719]	20446.1	24136.4	1.18049	
344	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	20446.1	24136.4	1.18049	
345	retinal short-chain dehydrogenase/reductase 3. [source:refseq;acc:nm_016246]	20446.1	24136.4	1.18049	
346	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [source:swissprot;acc:q8wyj6]	14229.2	16780.7	1.17931	
347	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [source:swissprot;acc:p98073]	4991.02	5885.09	1.17914	
348	splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [source:swissprot;acc:q13435]	4991.02	5885.09	1.17914	
349	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [source:swissprot;acc:o43143]	4714.85	5554.38	1.17806	
350	sedlin. [source:swissprot;acc:o14582]	17396.9	20483.9	1.17745	
351	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	17396.9	20483.9	1.17745	
352	bet3 homolog. [source:swissprot;acc:o43617]	17396.9	20483.9	1.17745	
353	p66 alpha. [source:refseq;acc:nm_017660]	12839	10911.1	1.17669	
354	transcription repressor p66 beta component of the mecp1 complex. [source:refseq;acc:nm_020699]	12839	10911.1	1.17669	
355	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [source:swissprot;acc:p17735]	12839	10911.1	1.17669	
356	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [source:swissprot;acc:p17987]	11004.2	12944.2	1.1763	
357	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [source:refseq;acc:nm_032549]	5061.11	5950.22	1.17567	
358	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [source:swissprot;acc:p21378]	5061.11	5950.22	1.17567	
359	cell division protein kinase 3 (ec 2.7.1.-). [source:swissprot;acc:q00526]	12798.9	10887.2	1.17559	
360	g2/mitotic-specific cyclin b2. [source:swissprot;acc:o95067]	12796.8	10886	1.17553	
361	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [source:swissprot;acc:p24941]	12787.6	10880.5	1.17528	
362	g2/mitotic-specific cyclin b1. [source:swissprot;acc:p14635]	12786.6	10879.9	1.17525	
363	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [source:swissprot;acc:p06493]	12780.7	10876.4	1.17509	
364	ptb domain adaptor protein ced-6; engulfment adapter protein. [source:refseq;acc:nm_016315]	5189	6088.47	1.17334	
365	calcyphosine. [source:swissprot;acc:q13938]	5189	6088.47	1.17334	
366	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [source:swissprot;acc:q9bzj0]	5189	6088.47	1.17334	
367	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [source:swissprot;acc:q07864]	4024.4	4719.35	1.17268	
368	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [source:swissprot;acc:o60508]	5082.66	5959.99	1.17261	
369	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [source:swissprot;acc:q03701]	3583.56	4194.95	1.17061	
370	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [source:swissprot;acc:p05455]	4108.15	4808.93	1.17058	
371	serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [source:swissprot;acc:o43464]	5067.02	5926.46	1.16961	
372	probable serine protease htra4 precursor (ec 3.4.21.-). [source:swissprot;acc:p83105]	5067	5926.17	1.16956	
373	probable serine protease htra3 precursor (ec 3.4.21.-). [source:swissprot;acc:p83110]	5066.99	5926.1	1.16955	
374	serine protease htra1 precursor (ec 3.4.21.-) (l56). [source:swissprot;acc:q92743]	5066.93	5925.38	1.16942	
375	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [source:swissprot;acc:o15116]	4700.42	5492.63	1.16854	
376	44050 protein. [source:refseq;acc:nm_178832]	17385.9	14889.2	1.16769	
377	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [source:swissprot;acc:q12972]	17385.9	14889.2	1.16769	
378	hira-interacting protein 5 (cgi-33). [source:swissprot;acc:q9ums0]	12471.7	14561.7	1.16758	
379	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [source:swissprot;acc:p31350]	6704.44	7811.45	1.16512	
380	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [source:swissprot;acc:p49748]	12998.5	15138.2	1.16461	
381	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [source:swissprot;acc:q12904]	5246.01	6109.31	1.16456	
382	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [source:refseq;acc:nm_004562]	4533.74	5279.4	1.16447	
383	hepatoma-derived growth factor-related protein 2. [source:refseq;acc:nm_032631]	4533.74	5279.4	1.16447	
384	cgi-142; hepatoma-derived growth factor 2. [source:refseq;acc:nm_016073]	4533.74	5279.4	1.16447	
385	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [source:refseq;acc:nm_033222]	4533.74	5279.4	1.16447	
386	60s ribosomal protein l8. [source:swissprot;acc:p25120]	4533.74	5279.4	1.16447	
387	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [source:swissprot;acc:p51858]	4533.74	5279.4	1.16447	
388	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [source:refseq;acc:nm_138574]	4533.74	5279.4	1.16447	
389	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [source:swissprot;acc:p26196]	4533.74	5279.4	1.16447	
390	rw1 protein (fragment). [source:swissprot;acc:q92545]	4533.74	5279.4	1.16447	
391	tar dna-binding protein-43 (tdp-43). [source:swissprot;acc:q13148]	3658.76	3144.39	1.16358	
392	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [source:refseq;acc:nm_024072]	3641.89	4236.95	1.16339	

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/