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 473 to 522 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
119	exocyst complex component sec5. [source:swissprot;acc:q96kp1]	Squared	210335	136716	1.53848	
119	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Measured	21185	28492	1.34491	
119	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [source:swissprot;acc:o43181]	Ranked	318.982	259.004	1.23157	
119	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [source:swissprot;acc:q99807]	Rooted	50.3247	62.9892	1.25166	
120	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [source:refseq;acc:nm_006339]	Measured	5136.78	6895.98	1.34247	
120	homer, neuronal immediate early gene, 1b. [source:refseq;acc:nm_004272]	Rooted	50.3333	62.9942	1.25154	
120	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [source:swissprot;acc:q9bwt3]	Squared	210199	136638	1.53836	
120	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [source:refseq;acc:nm_012281]	Ranked	269.278	327.709	1.21699	
121	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [source:swissprot;acc:p32929]	Ranked	269.254	327.655	1.2169	
121	homer, neuronal immediate early gene, 3. [source:refseq;acc:nm_004838]	Rooted	50.339	62.9975	1.25147	
121	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [source:swissprot;acc:p36873]	Squared	199594	130021	1.53509	
121	transcription factor jun-b. [source:swissprot;acc:p17275]	Measured	5579.18	7488.4	1.3422	
122	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [source:refseq;acc:nm_001326]	Squared	201896	131906	1.53061	
122	high-mobility group 20a. [source:refseq;acc:nm_018200]	Measured	5140.14	6893.53	1.34112	
122	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [source:refseq;acc:nm_004980]	Ranked	269.248	327.642	1.21688	
122	transcription factor jun-d. [source:swissprot;acc:p17535]	Rooted	63.636	79.6225	1.25122	
123	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Measured	24260.3	18172.1	1.33503	
123	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [source:swissprot;acc:p31483]	Rooted	54.6527	67.9743	1.24375	
123	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [source:refseq;acc:nm_004979]	Ranked	269.23	327.601	1.21681	
123	protein phosphatase inhibitor 2 (ipp-2). [source:swissprot;acc:p41236]	Squared	192904	126167	1.52896	
124	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [source:refseq;acc:nm_006339]	Ranked	208.52	171.595	1.21519	
124	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	Measured	24255.7	18168.9	1.33501	
124	nucleolysin tiar (tia-1 related protein). [source:swissprot;acc:q01085]	Rooted	54.6625	67.9477	1.24304	
124	type 1 protein phosphatase inhibitor. [source:refseq;acc:nm_025210]	Squared	192779	126095	1.52884	
125	high-mobility group 20a. [source:refseq;acc:nm_018200]	Ranked	208.588	171.778	1.21429	
125	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [source:swissprot;acc:q9h492]	Measured	24255.7	18168.9	1.33501	
125	ribosome biogenesis regulatory protein homolog. [source:swissprot;acc:q15050]	Squared	189976	124480	1.52616	
125	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [source:swissprot;acc:p13641]	Rooted	54.8203	67.934	1.23921	
126	associated molecule with the sh3 domain of stam (amsh) like protein. [source:refseq;acc:nm_020799]	Ranked	94	114	1.21277	
126	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Measured	24250	18164.9	1.33499	
126	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [source:refseq;acc:nm_006339]	Rooted	60.9342	75.1387	1.23311	
126	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [source:swissprot;acc:p08129]	Squared	189976	124480	1.52616	
127	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [source:swissprot;acc:p33551]	Squared	88432.6	58423.3	1.51365	
127	high-mobility group 20a. [source:refseq;acc:nm_018200]	Rooted	60.9353	75.094	1.23236	
127	putative breast adenocarcinoma marker (32kd). [source:refseq;acc:nm_014453]	Ranked	94	114	1.21277	
127	transcription factor jun-d. [source:swissprot;acc:p17535]	Measured	5638.2	7523.39	1.33436	
128	associated molecule with the sh3 domain of stam. [source:refseq;acc:nm_006463]	Ranked	94	114	1.21277	
128	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	Measured	4355.61	5810.82	1.3341	
128	pnas-18. [source:sptrembl;acc:q9bzu3]	Squared	87787.3	58155.8	1.50952	
128	tar dna-binding protein-43 (tdp-43). [source:swissprot;acc:q13148]	Rooted	48.0515	39.0445	1.23069	
129	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [source:sptrembl;acc:q8wwk2]	Rooted	54.2343	66.7323	1.23044	
129	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	Measured	4358.13	5811.49	1.33348	
129	neuroendocrine differentiation factor; comparative gene identification transcript 149. [source:refseq;acc:nm_016079]	Ranked	94	114	1.21277	
129	pre-mrna cleavage complex ii protein pcf11 (fragment). [source:swissprot;acc:o94913]	Squared	178263	118639	1.50257	
130	44050 protein. [source:refseq;acc:nm_178832]	Squared	148058	99628.4	1.4861	
130	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [source:refseq;acc:nm_138457]	Measured	2234.68	2978.53	1.33287	
130	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [source:refseq;acc:nm_017892]	Rooted	55.1026	67.5701	1.22626	
130	protein hspc134 (protein cda04). [source:swissprot;acc:q9by43]	Ranked	94	114	1.21277	
131	forkhead box protein p1 (hspc215). [source:swissprot;acc:q9h334]	Measured	2234.73	2978.57	1.33285	
131	huntingtin-interacting protein hypa/fbp11 (fragment). [source:sptrembl;acc:o75404]	Rooted	55.1113	67.5537	1.22577	

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/