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 501 to 550 of 7460 in total

Value Type	Measured
Interaction Map	High confidence

Rank	description	Network Comparison Type	Filtered	red	green	network_comparison	
126	calcyphosine. [source:swissprot;acc:q13938]	Divided	0	472.524	635.875	1.3457	
126	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Divided	1	24250	18164.9	1.33499	
126	pp3111 protein. [source:refseq;acc:nm_022156]	Subtracted	0	789	530	259	
126	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Subtracted	1	450.5	2394.5	1944	
127	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [source:swissprot;acc:p11766]	Subtracted	0	2017.91	1759.22	258.69	
127	lipopolysaccharide-binding protein precursor (lbp). [source:swissprot;acc:p18428]	Divided	0	86	64	1.34375	
127	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Subtracted	1	450.5	2394.5	1944	
127	transcription factor jun-d. [source:swissprot;acc:p17535]	Divided	1	5638.2	7523.39	1.33436	
128	importin 9. [source:refseq;acc:nm_018085]	Subtracted	0	1143.55	1397.66	254.11	
128	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	Divided	1	4355.61	5810.82	1.3341	
128	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [source:swissprot;acc:p82650]	Divided	0	81.504	60.8613	1.33918	
128	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [source:swissprot;acc:p17987]	Subtracted	1	11004.2	12944.2	1940	
129	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	Divided	1	4358.13	5811.49	1.33348	
129	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [source:swissprot;acc:q99733]	Subtracted	0	1143.55	1397.66	254.11	
129	protein hspc134 (protein cda04). [source:swissprot;acc:q9by43]	Divided	0	606.485	454.837	1.33341	
129	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [source:refseq;acc:nm_015316]	Subtracted	1	15274.9	13346.9	1928	
130	chromodomain y-like protein 2. [source:refseq;acc:nm_152342]	Subtracted	0	3053.31	2799.81	253.5	
130	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [source:refseq;acc:nm_138457]	Divided	1	2234.68	2978.53	1.33287	
130	maspin precursor (protease inhibitor 5). [source:swissprot;acc:p36952]	Divided	0	42	56	1.33333	
130	p66 alpha. [source:refseq;acc:nm_017660]	Subtracted	1	12839	10911.1	1927.9	
131	forkhead box protein p1 (hspc215). [source:swissprot;acc:q9h334]	Divided	1	2234.73	2978.57	1.33285	
131	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [source:swissprot;acc:p18031]	Subtracted	0	4912.01	4658.69	253.32	
131	serpin b11. [source:swissprot;acc:q96p15]	Divided	0	42	56	1.33333	
131	transcription repressor p66 beta component of the mecp1 complex. [source:refseq;acc:nm_020699]	Subtracted	1	12839	10911.1	1927.9	
132	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [source:swissprot;acc:p50452]	Divided	0	42	56	1.33333	
132	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [source:swissprot;acc:q9bzs1]	Divided	1	2236.61	2980.35	1.33253	
132	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [source:swissprot;acc:p17735]	Subtracted	1	12839	10911.1	1927.9	
132	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [source:swissprot;acc:q9uf02]	Subtracted	0	1949.36	2202	252.64	
133	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o95340]	Divided	0	252	335	1.32937	
133	cell division protein kinase 3 (ec 2.7.1.-). [source:swissprot;acc:q00526]	Subtracted	1	12798.9	10887.2	1911.7	
133	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	Divided	1	23421.5	17580.4	1.33225	
133	testis-specific chromodomain protein y protein 2. [source:swissprot;acc:q9y6f7]	Subtracted	0	3036.85	2784.59	252.26	
134	g2/mitotic-specific cyclin b2. [source:swissprot;acc:o95067]	Subtracted	1	12796.8	10886	1910.8	
134	gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]	Divided	1	21785.2	16426.1	1.32626	
134	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [source:refseq;acc:nm_022362]	Divided	0	260.986	346.751	1.32862	
134	testis-specific chromodomain y protein 1. [source:swissprot;acc:q9y6f8]	Subtracted	0	3036.29	2784.08	252.21	
135	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [source:swissprot;acc:p35268]	Subtracted	0	728.65	476.619	252.031	
135	apg3p; pc3-96 protein. [source:refseq;acc:nm_022488]	Divided	1	21785.2	16426.1	1.32626	
135	rna polymerase i transcription factor rrn3. [source:refseq;acc:nm_018427]	Divided	0	814.485	613.614	1.32736	
135	transcription factor jun-b. [source:swissprot;acc:p17275]	Subtracted	1	5579.18	7488.4	1909.22	
136	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [source:swissprot;acc:p24941]	Subtracted	1	12787.6	10880.5	1907.1	
136	glycine cleavage system h protein, mitochondrial precursor. [source:swissprot;acc:p23434]	Subtracted	0	903.767	1152.06	248.293	
136	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [source:swissprot;acc:q13952]	Divided	1	3620.77	4763.34	1.31556	
136	transcription factor e2f2 (e2f-2). [source:swissprot;acc:q14209]	Divided	0	1526.38	1150.51	1.3267	
137	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [source:swissprot;acc:p23511]	Divided	1	3620.77	4763.34	1.31556	
137	g2/mitotic-specific cyclin b1. [source:swissprot;acc:p14635]	Subtracted	1	12786.6	10879.9	1906.7	
137	heat shock factor binding protein 1. [source:swissprot;acc:o75506]	Divided	0	1631.18	1233.41	1.3225	
137	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [source:swissprot;acc:p23921]	Subtracted	0	7520.78	7276.12	244.66	
138	60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621]	Subtracted	0	1663.73	1906.28	242.55	
138	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [source:refseq;acc:nm_014592]	Divided	1	2755.15	2094.3	1.31555	

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/