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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2451 to 2500 of 25824 in total 
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	Value Type	Network Comparison Type	red	green	network_comparison	
307	CCT3	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [source:swissprot;acc:p49368]	Measured	Divided	12365.2	14824.9	1.19892	
307	GRAP2	grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [source:swissprot;acc:o75791]	Squared	Divided	28896.4	36766.8	1.27237	
307	MAGEA6	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [source:swissprot;acc:p43360]	Ranked	Subtracted	88.2482	110.265	22.0168	
307	SIN3A	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [source:refseq;acc:nm_015477]	Rooted	Divided	50.4687	45.2733	1.11476	
307	SRR	serine racemase (ec 5.1.1.-). [source:swissprot;acc:q9gzt4]	Ranked	Divided	242.153	266.673	1.10126	
307	WASL	neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401]	Rooted	Subtracted	66.0989	74.0609	7.962	
308	ADC	ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [source:swissprot;acc:q96a70]	Squared	Subtracted	32991.5	40704.5	7713	
308	AGPAT3	1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [source:swissprot;acc:q9nrz7]	Squared	Divided	30596.2	38919.9	1.27205	
308	BHLHB4	ba305p22.3 (breast carcinoma amplified sequence 4). [source:sptrembl;acc:q8ndy6]	Measured	Subtracted	11852.9	10773.5	1079.4	
308	DENR	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [source:swissprot;acc:o43583]	Rooted	Divided	50.4687	45.2733	1.11476	
308	DVL1	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [source:swissprot;acc:o14640]	Measured	Divided	4977.09	5966.44	1.19878	
308	NDN	necdin. [source:swissprot;acc:q99608]	Ranked	Subtracted	88.2482	110.265	22.0168	
308	RPL34	60s ribosomal protein l34. [source:swissprot;acc:p49207]	Ranked	Divided	242.153	266.673	1.10126	
308	RPS6KC1	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [source:refseq;acc:nm_012424]	Rooted	Subtracted	65.9938	73.9449	7.9511	
309		ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	Rooted	Subtracted	65.9938	73.9449	7.9511	
309		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]	Rooted	Divided	56.185	62.6036	1.11424	
309	AZIN1	ornithine decarboxylase antizyme inhibitor. [source:swissprot;acc:o14977]	Squared	Subtracted	32987.4	40698.5	7711.1	
309	BHLHB5	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [source:refseq;acc:nm_152414]	Measured	Subtracted	11848.8	10770.3	1078.5	
309	CUTL1	ccaat displacement protein (cdp) (cut-like 1). [source:swissprot;acc:p39880]	Squared	Divided	28900.8	36762.6	1.27203	
309	DVL2	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [source:swissprot;acc:o14641]	Measured	Divided	4977.8	5966.14	1.19855	
309	MAGED1	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [source:swissprot;acc:q9y5v3]	Ranked	Subtracted	88.2482	110.265	22.0168	
309	SEC61A2	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [source:swissprot;acc:q9y2r3]	Ranked	Divided	242.153	266.673	1.10126	
310		1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [source:swissprot;acc:q99943]	Measured	Subtracted	7551.8	8630.06	1078.26	
310		myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [source:swissprot;acc:p13533]	Rooted	Divided	95.0526	85.3206	1.11406	
310	C15orf15	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [source:refseq;acc:nm_016304]	Squared	Subtracted	30651.3	38253.3	7602	
310	CUTL2	homeobox protein cux-2 (cut-like 2) (fragment). [source:swissprot;acc:o14529]	Squared	Divided	28901.4	36762.1	1.27198	
310	MAGEF1	melanoma-associated antigen f1 (mage-f1 antigen). [source:swissprot;acc:q9hay2]	Ranked	Subtracted	88.2482	110.265	22.0168	
310	SART1	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	
310	SEC61A1	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [source:swissprot;acc:p38378]	Ranked	Divided	242.153	266.673	1.10126	
310	TXNL4A	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [source:swissprot;acc:o14834]	Rooted	Subtracted	56.9506	64.7888	7.8382	
311		40s ribosomal protein s28. [source:swissprot;acc:p25112]	Squared	Subtracted	30682.9	38183.6	7500.7	
311	AGPAT4	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	APBA1	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	DVL3	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [source:swissprot;acc:q92997]	Measured	Divided	4981.52	5964.58	1.19734	
311	EIF1B	protein translation factor sui1 homolog gc20. [source:swissprot;acc:o60739]	Ranked	Divided	242.627	267.151	1.10108	
311	MAGEB6B	melanoma antigen, family b, 6. [source:refseq;acc:nm_173523]	Ranked	Subtracted	88.2482	110.265	22.0168	
311	MYH4	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	RRM2B	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	
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		u6 snrna-associated sm-like protein lsm7. [source:swissprot;acc:q9uk45]	Measured	Divided	4598.21	5500.48	1.19622	
312	DNALI1	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	max protein. [source:swissprot;acc:p25912]	Measured	Subtracted	4640.26	5704.87	1064.61	
312	MYH8	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [source:swissprot;acc:p13535]	Rooted	Divided	95.0526	85.3206	1.11406	
312	NOSTRIN	nostrin. [source:refseq;acc:nm_052946]	Rooted	Subtracted	59.6399	51.9242	7.7157	
312	RPL3L	60s ribosomal protein l3-like. [source:swissprot;acc:q92901]	Ranked	Divided	242.195	266.663	1.10103	
313	DYNLT1	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	FBLN2	fibulin-2 precursor. [source:swissprot;acc:p98095]	Squared	Subtracted	45189.6	52666.2	7476.6	
313	LSM5	u6 snrna-associated sm-like protein lsm5. [source:swissprot;acc:q9y4y9]	Measured	Subtracted	4567.04	5631.2	1064.16	
313	MAGEA9	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	Ranked	Subtracted	88.2482	110.265	22.0168	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/