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 683 to 732 of 6456 in total 
Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
342	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [source:swissprot;acc:p09067]	Divided	20446.1	24136.4	1.18049	
342	steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [source:swissprot;acc:p11474]	Subtracted	10230.1	11256.2	1026.1	
343	homeobox protein hox-a5 (hox-1c). [source:swissprot;acc:p20719]	Divided	20446.1	24136.4	1.18049	
343	tuftelin-interacting protein 11 (hspc006). [source:swissprot;acc:q9ubb9]	Subtracted	4991.48	6014.08	1022.6	
344	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [source:refseq;acc:nm_138793]	Subtracted	9921.43	10941.2	1019.77	
344	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Divided	20446.1	24136.4	1.18049	
345	retinal short-chain dehydrogenase/reductase 3. [source:refseq;acc:nm_016246]	Divided	20446.1	24136.4	1.18049	
345	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [source:swissprot;acc:q8wxs5]	Subtracted	4068.78	5082.18	1013.4	
346	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [source:swissprot;acc:q8wyj6]	Divided	14229.2	16780.7	1.17931	
346	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [source:swissprot;acc:o60359]	Subtracted	4068.78	5082.18	1013.4	
347	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [source:swissprot;acc:p98073]	Divided	4991.02	5885.09	1.17914	
347	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [source:swissprot;acc:q9y698]	Subtracted	4068.82	5082.21	1013.39	
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]	Divided	4991.02	5885.09	1.17914	
348	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [source:swissprot;acc:q9ubn1]	Subtracted	4068.91	5082.27	1013.36	
349	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [source:swissprot;acc:o43143]	Divided	4714.85	5554.38	1.17806	
349	sad1/unc-84 protein-like 1. [source:swissprot;acc:o94901]	Subtracted	3349.9	4362.61	1012.71	
350	sedlin. [source:swissprot;acc:o14582]	Divided	17396.9	20483.9	1.17745	
350	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [source:swissprot;acc:q9uf02]	Subtracted	4074.83	5086.49	1011.66	
351	nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [source:swissprot;acc:q13232]	Subtracted	7878.27	8879.08	1000.81	
351	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	Divided	17396.9	20483.9	1.17745	
352	bet3 homolog. [source:swissprot;acc:o43617]	Divided	17396.9	20483.9	1.17745	
352	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [source:swissprot;acc:q15428]	Subtracted	4911.81	5909.18	997.37	
353	krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [source:swissprot;acc:q13887]	Subtracted	4911.81	5909.18	997.37	
353	p66 alpha. [source:refseq;acc:nm_017660]	Divided	12839	10911.1	1.17669	
354	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [source:swissprot;acc:p23921]	Subtracted	6913.6	7907.05	993.45	
354	transcription repressor p66 beta component of the mecp1 complex. [source:refseq;acc:nm_020699]	Divided	12839	10911.1	1.17669	
355	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [source:sptrembl;acc:q9nu36]	Subtracted	4914.27	5907.12	992.85	
355	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [source:swissprot;acc:p17735]	Divided	12839	10911.1	1.17669	
356	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [source:swissprot;acc:p17987]	Divided	11004.2	12944.2	1.1763	
356	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [source:swissprot;acc:p09661]	Subtracted	4914.27	5907.12	992.85	
357	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [source:refseq;acc:nm_032549]	Divided	5061.11	5950.22	1.17567	
357	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [source:swissprot;acc:o14640]	Subtracted	4977.09	5966.44	989.35	
358	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [source:swissprot;acc:p21378]	Divided	5061.11	5950.22	1.17567	
358	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [source:swissprot;acc:o14641]	Subtracted	4977.8	5966.14	988.34	
359	cell division protein kinase 3 (ec 2.7.1.-). [source:swissprot;acc:q00526]	Divided	12798.9	10887.2	1.17559	
359	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [source:swissprot;acc:o43181]	Subtracted	1920.75	2907.43	986.68	
360	g2/mitotic-specific cyclin b2. [source:swissprot;acc:o95067]	Divided	12796.8	10886	1.17553	
360	u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777]	Subtracted	4590.18	5575.52	985.34	
361	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [source:swissprot;acc:p22681]	Subtracted	6875.08	7858.38	983.3	
361	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [source:swissprot;acc:p24941]	Divided	12787.6	10880.5	1.17528	
362	g2/mitotic-specific cyclin b1. [source:swissprot;acc:p14635]	Divided	12786.6	10879.9	1.17525	
362	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [source:swissprot;acc:q92997]	Subtracted	4981.52	5964.58	983.06	
363	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [source:swissprot;acc:p06493]	Divided	12780.7	10876.4	1.17509	
363	signal transduction protein cbl-b (sh3-binding protein cbl-b). [source:swissprot;acc:q13191]	Subtracted	6856.71	7838.3	981.59	
364	dok-like protein. [source:refseq;acc:nm_024872]	Subtracted	6102.59	7081.46	978.87	
364	ptb domain adaptor protein ced-6; engulfment adapter protein. [source:refseq;acc:nm_016315]	Divided	5189	6088.47	1.17334	
365	calcyphosine. [source:swissprot;acc:q13938]	Divided	5189	6088.47	1.17334	
365	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [source:swissprot;acc:o60496]	Subtracted	6102.59	7081.46	978.87	
366	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [source:swissprot;acc:q9bzj0]	Divided	5189	6088.47	1.17334	
366	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [source:swissprot;acc:q99704]	Subtracted	6102.59	7081.46	978.87	

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/