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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Value Type Rank Filtered Gene description Network Comparison Type Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 38536 in total 
Value Type	Measured
Network Comparison Type	Divided

Rank	Filtered	description	Interaction Map	red	green	network_comparison	
126	0	calcyphosine. [source:swissprot;acc:q13938]	High confidence	472.524	635.875	1.3457	
126	0	fos-related antigen 2. [source:swissprot;acc:p15408]	Low confidence	3205.98	2407.27	1.33179	
126	1	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	High confidence	24250	18164.9	1.33499	
126	1	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]	Low confidence	11285.3	10318.5	1.0937	
127	0	lipopolysaccharide-binding protein precursor (lbp). [source:swissprot;acc:p18428]	High confidence	86	64	1.34375	
127	0	ubiquinol-cytochrome c reductase complex 7.2 kda protein (ec 1.10.2.2) (cytochrome c1, nonheme 7 kda protein) (complex iii subunit x) (7.2 kda cytochrome c1-associated protein subunit) (hspc119). [source:swissprot;acc:q9udw1]	Low confidence	680.5	511.5	1.3304	
127	1	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [source:swissprot;acc:p43355]	Low confidence	11285.3	10318.5	1.0937	
127	1	transcription factor jun-d. [source:swissprot;acc:p17535]	High confidence	5638.2	7523.39	1.33436	
128	0	double-stranded rna-specific editase 1 (ec 3.5.-.-) (dsrna adenosine deaminase) (rna editing deaminase 1) (rna editing enzyme 1). [source:swissprot;acc:p78563]	Low confidence	294	391	1.32993	
128	0	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [source:swissprot;acc:p82650]	High confidence	81.504	60.8613	1.33918	
128	1	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	High confidence	4355.61	5810.82	1.3341	
128	1	melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]	Low confidence	11285.3	10318.5	1.0937	
129	0	amiloride-sensitive sodium channel delta-subunit (epithelial na+ channel delta subunit) (delta enac) (nonvoltage-gated sodium channel 1 delta subunit) (scned) (delta nach). [source:swissprot;acc:p51172]	Low confidence	146.219	194.326	1.32901	
129	0	protein hspc134 (protein cda04). [source:swissprot;acc:q9by43]	High confidence	606.485	454.837	1.33341	
129	1	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	High confidence	4358.13	5811.49	1.33348	
129	1	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [source:swissprot;acc:p43366]	Low confidence	11285.3	10318.5	1.0937	
130	0	maspin precursor (protease inhibitor 5). [source:swissprot;acc:p36952]	High confidence	42	56	1.33333	
130	0	phosphatidylinositol 4-kinase alpha (ec 2.7.1.67) (pi4-kinase) (ptdins-4-kinase) (pi4k-alpha). [source:swissprot;acc:p42356]	Low confidence	707.801	937.501	1.32453	
130	1	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [source:refseq;acc:nm_138457]	High confidence	2234.68	2978.53	1.33287	
130	1	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [source:swissprot;acc:q9unf1]	Low confidence	11285.3	10318.5	1.0937	
131	0	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	Low confidence	645.504	851.77	1.31954	
131	0	serpin b11. [source:swissprot;acc:q96p15]	High confidence	42	56	1.33333	
131	1	forkhead box protein p1 (hspc215). [source:swissprot;acc:q9h334]	High confidence	2234.73	2978.57	1.33285	
131	1	trophinin. [source:swissprot;acc:q12816]	Low confidence	11285.3	10318.5	1.0937	
132	0	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [source:swissprot;acc:p50452]	High confidence	42	56	1.33333	
132	0	wd-repeat protein 5 (wd-repeat protein big-3). [source:swissprot;acc:q9ugp9]	Low confidence	251.947	191.971	1.31242	
132	1	dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [source:swissprot;acc:p45985]	Low confidence	5948.88	5441.83	1.09318	
132	1	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [source:swissprot;acc:q9bzs1]	High confidence	2236.61	2980.35	1.33253	
133	0	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]	High confidence	252	335	1.32937	
133	0	cdc42-binding protein kinase beta; cdc42-binding protein kinase beta (dmpk-like); mrck beta; dmpk-like. [source:refseq;acc:nm_006035]	Low confidence	874	1139	1.3032	
133	1	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	High confidence	23421.5	17580.4	1.33225	
133	1	ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	Low confidence	7013	7662.77	1.09265	
134	0	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [source:refseq;acc:nm_022362]	High confidence	260.986	346.751	1.32862	
134	0	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [source:swissprot;acc:q8tct7]	Low confidence	874	1139	1.3032	
134	1	ba127l20.1 (novel glutathione-s-transferase). [source:sptrembl;acc:q9h4y5]	Low confidence	6670.21	7286.66	1.09242	
134	1	gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]	High confidence	21785.2	16426.1	1.32626	
135	0	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [source:swissprot;acc:q14168]	Low confidence	265.513	203.832	1.30261	
135	0	rna polymerase i transcription factor rrn3. [source:refseq;acc:nm_018427]	High confidence	814.485	613.614	1.32736	
135	1	apg3p; pc3-96 protein. [source:refseq;acc:nm_022488]	High confidence	21785.2	16426.1	1.32626	
135	1	high-mobility group 20a. [source:refseq;acc:nm_018200]	Low confidence	7248.24	7916.96	1.09226	
136	0	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [source:swissprot;acc:p18577]	Low confidence	200.834	154.324	1.30138	
136	0	transcription factor e2f2 (e2f-2). [source:swissprot;acc:q14209]	High confidence	1526.38	1150.51	1.3267	
136	1	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]	High confidence	3620.77	4763.34	1.31556	
136	1	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [source:refseq;acc:nm_012424]	Low confidence	7020.48	7667.34	1.09214	
137	0	blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [source:swissprot;acc:q02161]	Low confidence	200.759	154.279	1.30127	
137	0	heat shock factor binding protein 1. [source:swissprot;acc:o75506]	High confidence	1631.18	1233.41	1.3225	
137	1	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]	High confidence	3620.77	4763.34	1.31556	
137	1	t-box transcription factor tbx19 (t-box protein 19). [source:swissprot;acc:o60806]	Low confidence	6139.6	6699.58	1.09121	
138	0	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [source:swissprot;acc:p18577]	Low confidence	200.759	154.279	1.30127	
138	0	ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [source:swissprot;acc:p47986]	High confidence	204.382	154.804	1.32026	

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/