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 712 to 761 of 3730 in total

Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	Filtered	red	green	network_comparison	
356	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [source:swissprot;acc:p43358]	0	16321	15577	1.04776	
357	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	1	243.12	266.661	1.09683	
357	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	0	16321	15577	1.04776	
358	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	0	16321	15577	1.04776	
358	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	1	243.12	266.662	1.09683	
359	60s ribosomal protein l4 (l1). [source:swissprot;acc:p36578]	1	239.277	262.434	1.09678	
359	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	0	16321	15577	1.04776	
360	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]	0	16321	15577	1.04776	
360	protein transport protein sec61 gamma subunit. [source:swissprot;acc:p38384]	1	243.072	266.559	1.09663	
361	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [source:swissprot;acc:p43355]	0	16321	15577	1.04776	
361	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [source:refseq;acc:nm_022061]	1	242.83	266.248	1.09644	
362	apical-like protein (apxl protein). [source:swissprot;acc:q13796]	1	231.492	211.136	1.09641	
362	melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]	0	16321	15577	1.04776	
363	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [source:swissprot;acc:p43366]	0	16321	15577	1.04776	
363	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [source:refseq;acc:nm_020859]	1	231.481	211.131	1.09639	
364	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [source:swissprot;acc:p30876]	1	243.208	266.617	1.09625	
364	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]	0	16321	15577	1.04776	
365	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [source:swissprot;acc:q9p0j6]	1	242.744	266.07	1.09609	
365	transcription factor e2f2 (e2f-2). [source:swissprot;acc:q14209]	0	7769.96	8139.71	1.04759	
366	40s ribosomal protein s5. [source:swissprot;acc:p46782]	1	242.473	265.756	1.09602	
366	glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [source:swissprot;acc:p23378]	0	8614.89	9017.27	1.04671	
367	f-actin capping protein alpha-2 subunit (capz alpha-2). [source:swissprot;acc:p47755]	0	13801.7	13185.9	1.0467	
367	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [source:swissprot;acc:p52272]	1	234.146	256.627	1.09601	
368	adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [source:swissprot;acc:p56377]	0	16679.2	15940.6	1.04633	
368	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [source:swissprot;acc:q9y606]	1	242.66	265.715	1.09501	
369	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [source:swissprot;acc:p80404]	0	18849.7	19704.7	1.04536	
369	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [source:swissprot;acc:p52815]	1	242.159	265.104	1.09475	
370	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [source:refseq;acc:nm_031438]	1	242.159	265.104	1.09475	
370	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [source:swissprot;acc:p29803]	0	13652.7	13061	1.0453	
371	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [source:refseq;acc:nm_012424]	1	186.52	170.42	1.09447	
371	swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [source:refseq;acc:nm_003075]	0	13247.9	12674.2	1.04527	
372	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [source:refseq;acc:nm_016355]	0	11869.9	12402.7	1.04489	
372	ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	1	186.52	170.42	1.09447	
373	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [source:swissprot;acc:q9y3b7]	1	242.37	265.255	1.09442	
373	mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [source:swissprot;acc:q99683]	0	10598.2	11061.5	1.04371	
374	calcyphosine. [source:swissprot;acc:q13938]	0	9874.54	9478.1	1.04183	
374	transcription factor dp-2 (e2f dimerization partner 2). [source:swissprot;acc:q14188]	1	267.208	244.168	1.09436	
375	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [source:swissprot;acc:o14802]	1	242.686	265.516	1.09407	
375	tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [source:refseq;acc:nm_015975]	0	14247.6	13686.9	1.04097	
376	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [source:swissprot;acc:q9ny93]	1	257.017	234.945	1.09395	
376	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [source:swissprot;acc:p31930]	0	10284.9	10695.6	1.03993	
377	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [source:swissprot;acc:o95602]	1	242.691	265.481	1.09391	
377	integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [source:swissprot;acc:p05106]	0	14512.3	13958.2	1.0397	
378	60s ribosomal protein l30. [source:swissprot;acc:p04645]	1	242.593	265.365	1.09387	
378	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [source:swissprot;acc:q96jq0]	0	19713.5	18962.5	1.0396	
379	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	0	11228.4	10806	1.03909	
379	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p54819]	1	241.509	264.163	1.0938	
380	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [source:swissprot;acc:p42677]	0	9566.15	9936.37	1.0387	
380	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [source:refseq;acc:nm_003169]	1	242.109	264.79	1.09368	
381	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [source:refseq;acc:nm_015920]	0	9565.54	9935.19	1.03864	

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/