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 2908 to 2957 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
364	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	Ranked	0	16321	15577	1.04776
		Squared	0	0.545325	0.615621	1.12891
	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	Measured	1	5189	6088.47	1.17334
	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	Squared	1	17957.2	22234.1	1.23817
	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	Rooted	0	53.8642	56.248	1.04426
365	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	Ranked	1	242.744	266.07	1.09609
	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	Squared		17965.8	22243	1.23807
	calcyphosine. [swissprot;acc:q13938]	Measured		5189	6088.47	1.17334
	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	Rooted	0	30.3712	31.6971	1.04366
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Measured	0	48	51	1.0625
	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	Rooted	1	49.7541	54.9425	1.10428
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Ranked	0	7769.96	8139.71	1.04759
	tubby protein homolog. [swissprot;acc:p50607]	Squared	0	9661.54	10902.9	1.12848
366	40s ribosomal protein s15a. [swissprot;acc:p39027]	Rooted	1	50.5463	45.7763	1.1042
	40s ribosomal protein s5. [swissprot;acc:p46782]	Ranked		242.473	265.756	1.09602
	ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	Squared		62783.5	50784.1	1.23628
	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	Measured		5189	6088.47	1.17334
	glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378]	Ranked	0	8614.89	9017.27	1.04671
	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	Measured		48	51	1.0625
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Squared		4339.93	3865.57	1.12271
	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]	Rooted		45.1768	47.1159	1.04292
367	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	Rooted	1	49.0882	54.2027	1.10419
	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414]	Squared		62757.7	50767.8	1.23617
	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864]	Measured		4024.4	4719.35	1.17268
	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	Measured	0	2039.47	2164.92	1.06151
	f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755]	Ranked		13801.7	13185.9	1.0467
	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	Squared		72128.6	64272.5	1.12223
	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	Ranked	1	234.146	256.627	1.09601
	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]	Rooted	0	45.1768	47.1159	1.04292
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). [swissprot;acc:p56377]	Ranked		16679.2	15940.6	1.04633
	aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]	Rooted		17.8274	17.1002	1.04253
	dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442]	Squared	1	51805.2	41916.4	1.23592
	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	Measured	0	5946.96	5606.29	1.06077
	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]	Rooted	1	49.5225	54.6817	1.10418
	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	Measured	1	5082.66	5959.99	1.17261
	ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154]	Squared	0	346.699	309.317	1.12085
	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	Ranked	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). [swissprot;acc:p80404]		0	18849.7	19704.7	1.04536
	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]		1	242.159	265.104	1.09475
	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	Measured	1	3583.56	4194.95	1.17061
	dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325]	Measured	0	1048.65	988.882	1.06044
	galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182]	Squared	1	45960.8	56749.6	1.23474
	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]	Rooted	1	49.7435	45.0586	1.10397
	ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658]	Squared	0	346.699	309.317	1.12085
	uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452]	Rooted		17.8274	17.1002	1.04253
370	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	Rooted		30.7424	32.0298	1.04188
	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]	Measured		1049.21	989.438	1.06041
	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	Measured	1	4108.15	4808.93	1.17058
	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579]	Rooted		49.7435	45.0586	1.10397
	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]	Ranked		242.159	265.104	1.09475

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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/