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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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 575 to 624 of 3730 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	Filtered	red	green	network_comparison	
288	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [source:swissprot;acc:q9ukf6]	1	23422.4	19380.3	1.20857	
288	likely ortholog of mouse shc sh2-domain binding protein 1. [source:refseq;acc:nm_024745]	0	1293.73	1161.64	1.11371	
289	tubby protein homolog. [source:swissprot;acc:p50607]	0	3797.57	4228.27	1.11341	
289	u6 snrna-associated sm-like protein lsm6 (sm protein f). [source:swissprot;acc:q9y4y8]	1	4682.88	5646.19	1.20571	
290	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [source:swissprot;acc:q02880]	0	1370.82	1525.56	1.11288	
290	tuftelin-interacting protein 11 (hspc006). [source:swissprot;acc:q9ubb9]	1	4991.48	6014.08	1.20487	
291	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	1	44490.5	36927.5	1.20481	
291	similar to ribosomal protein, large, p0. [source:sptrembl;acc:q96fq9]	0	1961.09	2179.77	1.11151	
292	ba271b5.1 (similar to ribosomal protein s7). [source:sptrembl;acc:q9h1s9]	0	11223	12473	1.11138	
292	nucleotide-binding protein 1 (nbp 1). [source:swissprot;acc:p53384]	1	4641.09	5588.75	1.20419	
293	block 23. [source:sptrembl;acc:q8nhw5]	0	1943.32	2159.55	1.11127	
293	nucleotide binding protein 2 (nbp 2). [source:swissprot;acc:q9y5y2]	1	4641.09	5588.75	1.20419	
294	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [source:refseq;acc:nm_001326]	1	22515.5	18702.6	1.20387	
294	mesoderm induction early response 1. [source:refseq;acc:nm_020948]	0	1914.5	1723.5	1.11082	
295	adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [source:swissprot;acc:q9y6q5]	0	426.8	384.843	1.10902	
295	ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [source:swissprot;acc:q9nzl6]	1	13261.9	11017.8	1.20368	
296	pnas-18. [source:sptrembl;acc:q9bzu3]	0	2256.05	2035.28	1.10847	
296	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [source:swissprot;acc:q15428]	1	4911.81	5909.18	1.20306	
297	40s ribosomal protein s29. [source:swissprot;acc:p30054]	0	1711.6	1895.38	1.10737	
297	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]	1	4911.81	5909.18	1.20306	
298	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [source:swissprot;acc:q9y333]	1	4633.92	5572.85	1.20262	
298	williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [source:swissprot;acc:q9np71]	0	939	848	1.10731	
299	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [source:sptrembl;acc:q9nu36]	1	4914.27	5907.12	1.20203	
299	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [source:swissprot;acc:p33551]	0	2231.05	2015.09	1.10717	
300	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [source:swissprot;acc:q12772]	0	1334.19	1205.1	1.10712	
300	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [source:swissprot;acc:p09661]	1	4914.27	5907.12	1.20203	
301	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [source:swissprot;acc:p33551]	1	13768.2	11466	1.20078	
301	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [source:swissprot;acc:q14488]	0	135.294	149.371	1.10405	
302	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [source:refseq;acc:nm_016123]	0	135.294	149.371	1.10405	
302	pallidin; pallid (mouse) homolog, pallidin. [source:refseq;acc:nm_012388]	1	5894.75	7073.65	1.19999	
303	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [source:swissprot;acc:p36873]	1	22268.8	18560.4	1.1998	
303	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [source:refseq;acc:nm_014633]	0	952.488	863.886	1.10256	
304	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [source:refseq;acc:nm_015629]	1	4855.46	5824.52	1.19958	
304	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [source:swissprot;acc:q9nyl9]	0	4962.34	5469.68	1.10224	
305	odd-skipped related 1; odz (odd oz/ten-m) related 1. [source:refseq;acc:nm_145260]	1	3856.29	4624.15	1.19912	
305	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [source:swissprot;acc:q9y5x1]	0	4962.34	5469.68	1.10224	
306	glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [source:swissprot;acc:q06210]	0	1705.19	1547.2	1.10211	
306	pnas-18. [source:sptrembl;acc:q9bzu3]	1	13680.5	11409.6	1.19903	
307	ferritin heavy polypeptide-like 17. [source:swissprot;acc:q9bxu8]	0	4159.87	3775.43	1.10183	
307	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [source:swissprot;acc:p49368]	1	12365.2	14824.9	1.19892	
308	neurocalcin delta. [source:swissprot;acc:p29554]	0	702.055	773.218	1.10136	
308	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [source:swissprot;acc:o14640]	1	4977.09	5966.44	1.19878	
309	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [source:swissprot;acc:o14641]	1	4977.8	5966.14	1.19855	
309	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [source:refseq;acc:nm_003169]	0	1890.86	2081.91	1.10104	
310	purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [source:swissprot;acc:p00491]	0	4755.32	4320.09	1.10075	
310	squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [source:refseq;acc:nm_005146]	1	4909.79	5878.79	1.19736	
311	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [source:swissprot;acc:q92997]	1	4981.52	5964.58	1.19734	
311	transcription factor cp2; transcription factor cp2, alpha globin. [source:refseq;acc:nm_005653]	0	3117.17	2833.94	1.09994	
312	dyskerin (nucleolar protein nap57) (cbf5 homolog). [source:swissprot;acc:o60832]	0	3455.43	3800.29	1.0998	
312	u6 snrna-associated sm-like protein lsm7. [source:swissprot;acc:q9uk45]	1	4598.21	5500.48	1.19622	

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/