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 2480 to 2529 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
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]	Measured	Divided	4909.79	5878.79	1.19736	
311	1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [source:swissprot;acc:q9nrz5]	Squared	Divided	30566.4	38866.5	1.27154	
311	40s ribosomal protein s28. [source:swissprot;acc:p25112]	Squared	Subtracted	30682.9	38183.6	7500.7	
311	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [source:swissprot;acc:q02410]	Measured	Subtracted	2820.51	3897.1	1076.59	
311	melanoma antigen, family b, 6. [source:refseq;acc:nm_173523]	Ranked	Subtracted	88.2482	110.265	22.0168	
311	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [source:swissprot;acc:q9y623]	Rooted	Divided	95.0526	85.3206	1.11406	
311	protein translation factor sui1 homolog gc20. [source:swissprot;acc:o60739]	Ranked	Divided	242.627	267.151	1.10108	
311	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	Rooted	Subtracted	62.3337	70.0738	7.7401	
311	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [source:swissprot;acc:q92997]	Measured	Divided	4981.52	5964.58	1.19734	
312	60s ribosomal protein l3-like. [source:swissprot;acc:q92901]	Ranked	Divided	242.195	266.663	1.10103	
312	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [source:swissprot;acc:o14645]	Squared	Subtracted	33044.3	40524.8	7480.5	
312	max protein. [source:swissprot;acc:p25912]	Measured	Subtracted	4640.26	5704.87	1064.61	
312	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [source:swissprot;acc:p43358]	Ranked	Subtracted	88.2482	110.265	22.0168	
312	methyltransferase like 2. [source:refseq;acc:nm_018396]	Squared	Divided	71576.8	56326.7	1.27074	
312	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [source:swissprot;acc:p13535]	Rooted	Divided	95.0526	85.3206	1.11406	
312	nostrin. [source:refseq;acc:nm_052946]	Rooted	Subtracted	59.6399	51.9242	7.7157	
312	u6 snrna-associated sm-like protein lsm7. [source:swissprot;acc:q9uk45]	Measured	Divided	4598.21	5500.48	1.19622	
313	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [source:swissprot;acc:q15763]	Squared	Divided	71576.8	56326.7	1.27074	
313	eap30 subunit of ell complex. [source:refseq;acc:nm_007241]	Rooted	Subtracted	59.6399	51.9242	7.7157	
313	fibulin-2 precursor. [source:swissprot;acc:p98095]	Squared	Subtracted	45189.6	52666.2	7476.6	
313	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	Ranked	Subtracted	88.2482	110.265	22.0168	
313	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	Rooted	Divided	95.0526	85.3206	1.11406	
313	protein phosphatase inhibitor 2 (ipp-2). [source:swissprot;acc:p41236]	Measured	Divided	21644.2	18098.7	1.1959	
313	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	Ranked	Divided	232.473	211.207	1.10069	
313	u6 snrna-associated sm-like protein lsm5. [source:swissprot;acc:q9y4y9]	Measured	Subtracted	4567.04	5631.2	1064.16	
314	fzr1 protein; fizzy-related protein; cdc20-like 1b. [source:refseq;acc:nm_016263]	Squared	Divided	71576.8	56326.7	1.27074	
314	liv-1 protein, estrogen regulated. [source:refseq;acc:nm_012319]	Rooted	Subtracted	59.6399	51.9242	7.7157	
314	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	Ranked	Subtracted	88.2482	110.265	22.0168	
314	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [source:swissprot;acc:p53582]	Ranked	Divided	244.126	268.604	1.10027	
314	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [source:swissprot;acc:p11055]	Rooted	Divided	95.0526	85.3206	1.11406	
314	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	Measured	Subtracted	6563.65	7627.29	1063.64	
314	ring finger protein 25 (ec 6.3.2.-). [source:swissprot;acc:q96bh1]	Squared	Subtracted	51519.3	44060.4	7458.9	
314	type 1 protein phosphatase inhibitor. [source:refseq;acc:nm_025210]	Measured	Divided	21632.5	18090	1.19583	
315	arginyl-trna synthetase-like; arginine-trna ligase. [source:refseq;acc:nm_020320]	Squared	Subtracted	31819.7	39222.2	7402.5	
315	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [source:swissprot;acc:q05329]	Rooted	Subtracted	59.6399	51.9242	7.7157	
315	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	Ranked	Subtracted	88.2482	110.265	22.0168	
315	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [source:swissprot;acc:p50579]	Ranked	Divided	244.126	268.604	1.10027	
315	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [source:swissprot;acc:p12882]	Rooted	Divided	95.0526	85.3206	1.11406	
315	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [source:swissprot;acc:q92824]	Squared	Divided	71576.8	56326.7	1.27074	
315	ribosome biogenesis regulatory protein homolog. [source:swissprot;acc:q15050]	Measured	Divided	21370.8	17896.5	1.19413	
315	vav proto-oncogene. [source:swissprot;acc:p15498]	Measured	Subtracted	6644.99	7707.8	1062.81	
316	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [source:swissprot;acc:q99747]	Rooted	Subtracted	59.6399	51.9242	7.7157	
316	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]	Ranked	Subtracted	88.2482	110.265	22.0168	
316	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [source:swissprot;acc:p12883]	Rooted	Divided	95.0526	85.3206	1.11406	
316	neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401]	Squared	Divided	28918.3	36746	1.27068	
316	protein translation factor sui1 homolog (sui1iso1). [source:swissprot;acc:p41567]	Ranked	Divided	242.694	267.017	1.10022	
316	regulator of chromosome condensation (cell cycle regulatory protein). [source:swissprot;acc:p18754]	Squared	Subtracted	44848.2	52108.3	7260.1	
316	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [source:swissprot;acc:p08129]	Measured	Divided	21370.8	17896.5	1.19413	
316	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [source:swissprot;acc:o43516]	Measured	Subtracted	6603.41	7664.65	1061.24	
317	adiponectin receptor 2. [source:refseq;acc:nm_024551]	Measured	Divided	3153.1	3762.56	1.19329	

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/