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 312 to 361 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
312	u6 snrna-associated sm-like protein lsm7. [source:swissprot;acc:q9uk45]	4598.21	5500.48	1.19622	
313	protein phosphatase inhibitor 2 (ipp-2). [source:swissprot;acc:p41236]	21644.2	18098.7	1.1959	
314	type 1 protein phosphatase inhibitor. [source:refseq;acc:nm_025210]	21632.5	18090	1.19583	
315	ribosome biogenesis regulatory protein homolog. [source:swissprot;acc:q15050]	21370.8	17896.5	1.19413	
316	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [source:swissprot;acc:p08129]	21370.8	17896.5	1.19413	
317	adiponectin receptor 2. [source:refseq;acc:nm_024551]	3153.1	3762.56	1.19329	
318	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	34190.9	40795.8	1.19318	
319	ras-related gtp binding a; ras-related gtp-binding protein. [source:refseq;acc:nm_006570]	20911	24908.5	1.19117	
320	ras-related gtp binding c; rag c protein. [source:refseq;acc:nm_022157]	20911	24908.5	1.19117	
321	ras-related gtp binding b short isoform; gtp-binding protein ragb. [source:refseq;acc:nm_006064]	20911	24908.5	1.19117	
322	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [source:refseq;acc:nm_018685]	20911	24908.5	1.19117	
323	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [source:swissprot;acc:q9y4z0]	4620.76	5501.94	1.1907	
324	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	28136.5	33457.6	1.18912	
325	septin-like protein kiaa0202 (fragment). [source:swissprot;acc:q92599]	16177.9	19235.4	1.18899	
326	atp-dependent rna helicase ddx24 (dead-box protein 24). [source:swissprot;acc:q9gzr7]	3432.96	4081.21	1.18883	
327	septin 10 isoform 1. [source:refseq;acc:nm_144710]	16067.4	19094.4	1.18839	
328	brain protein 44. [source:swissprot;acc:o95563]	15999.1	19007.1	1.18801	
329	septin 7 (cdc10 protein homolog). [source:swissprot;acc:q16181]	15999.1	19007.1	1.18801	
330	septin 6. [source:swissprot;acc:q14141]	15959.9	18957.1	1.1878	
331	pre-mrna cleavage complex ii protein pcf11 (fragment). [source:swissprot;acc:o94913]	20287.2	17083.8	1.18751	
332	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [source:refseq;acc:nm_002669]	5051.16	5975.51	1.183	
333	nuclear matrix protein nmp200 related to splicing factor prp19. [source:refseq;acc:nm_014502]	5039.63	5961.83	1.18299	
334	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [source:swissprot;acc:o43236]	14924.4	17655.2	1.18298	
335	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [source:swissprot;acc:q9ny93]	3494.31	4129.6	1.18181	
336	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [source:swissprot;acc:q9nr33]	3751.3	4431.34	1.18128	
337	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	20446.1	24136.4	1.18049	
338	homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]	20446.1	24136.4	1.18049	
339	homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]	20446.1	24136.4	1.18049	
340	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	20446.1	24136.4	1.18049	
341	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [source:swissprot;acc:p09016]	20446.1	24136.4	1.18049	
342	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [source:swissprot;acc:p09067]	20446.1	24136.4	1.18049	
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	

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/