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 2951 to 3000 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
369	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [source:swissprot;acc:q9ul62]	Rooted	Subtracted	63.0663	56.4667	6.5996	
369	sorcin (22 kda protein) (cp-22) (v19). [source:swissprot;acc:p30626]	Squared	Subtracted	29096	35338.7	6242.7	
370	grancalcin. [source:swissprot;acc:p28676]	Squared	Subtracted	29095.7	35338.3	6242.6	
370	grb2-related adaptor protein. [source:swissprot;acc:q13588]	Rooted	Subtracted	61.4282	68.0107	6.5825	
370	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [source:swissprot;acc:p05455]	Measured	Divided	4108.15	4808.93	1.17058	
370	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [source:swissprot;acc:p50579]	Rooted	Divided	49.7435	45.0586	1.10397	
370	muscle-specific beta 1 integrin binding protein. [source:refseq;acc:nm_014446]	Ranked	Subtracted	218.818	238.358	19.54	
370	nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [source:swissprot;acc:p22392]	Measured	Subtracted	7753.59	8728.13	974.54	
370	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [source:refseq;acc:nm_031438]	Ranked	Divided	242.159	265.104	1.09475	
370	protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [source:swissprot;acc:p11171]	Squared	Divided	45986	56776.1	1.23464	
371	band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [source:swissprot;acc:q9h4g0]	Squared	Divided	45985.9	56776	1.23464	
371	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [source:swissprot;acc:p04632]	Squared	Subtracted	29095.3	35337.6	6242.3	
371	neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [source:refseq;acc:nm_145117]	Rooted	Subtracted	61.3383	67.8668	6.5285	
371	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [source:swissprot;acc:p46059]	Ranked	Subtracted	186.172	166.661	19.511	
371	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [source:refseq;acc:nm_015629]	Measured	Subtracted	4855.46	5824.52	969.06	
371	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [source:refseq;acc:nm_012424]	Ranked	Divided	186.52	170.42	1.09447	
371	serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [source:swissprot;acc:o43464]	Measured	Divided	5067.02	5926.46	1.16961	
371	zinc finger-like protein 9. [source:refseq;acc:nm_033414]	Rooted	Divided	49.3451	54.4606	1.10367	
372	band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [source:swissprot;acc:q9y2j2]	Squared	Divided	45986.7	56776.8	1.23464	
372	membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [source:swissprot;acc:q9umx9]	Rooted	Divided	49.3451	54.4606	1.10367	
372	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [source:refseq;acc:nm_014903]	Rooted	Subtracted	61.3354	67.8623	6.5269	
372	polymerase (rna) iii (dna directed) (32kd). [source:refseq;acc:nm_006467]	Ranked	Subtracted	239.709	259.038	19.329	
372	ponsin; sh3-domain protein 5 (ponsin). [source:refseq;acc:nm_015385]	Squared	Subtracted	29335.6	35515.5	6179.9	
372	probable serine protease htra4 precursor (ec 3.4.21.-). [source:swissprot;acc:p83105]	Measured	Divided	5067	5926.17	1.16956	
372	ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	Ranked	Divided	186.52	170.42	1.09447	
372	squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [source:refseq;acc:nm_005146]	Measured	Subtracted	4909.79	5878.79	969	
373	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [source:swissprot;acc:q9y3b7]	Ranked	Divided	242.37	265.255	1.09442	
373	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [source:refseq;acc:nm_021069]	Squared	Subtracted	28863.2	35031.5	6168.3	
373	band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [source:swissprot;acc:o43491]	Squared	Divided	45986	56776.1	1.23464	
373	dynactin 4. [source:refseq;acc:nm_032486]	Ranked	Subtracted	233.142	252.253	19.111	
373	guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [source:swissprot;acc:p36915]	Rooted	Divided	49.3451	54.4606	1.10367	
373	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [source:refseq;acc:nm_020443]	Rooted	Subtracted	61.3354	67.8621	6.5267	
373	probable serine protease htra3 precursor (ec 3.4.21.-). [source:swissprot;acc:p83110]	Measured	Divided	5066.99	5926.1	1.16955	
373	u6 snrna-associated sm-like protein lsm6 (sm protein f). [source:swissprot;acc:q9y4y8]	Measured	Subtracted	4682.88	5646.19	963.31	
374	60s ribosomal protein l26. [source:swissprot;acc:q02877]	Rooted	Divided	50.2549	45.5599	1.10305	
374	e2a-pbx1-associated protein; putative 47 kda protein. [source:refseq;acc:nm_020140]	Rooted	Subtracted	61.3352	67.8618	6.5266	
374	electron transfer flavoprotein beta-subunit (beta-etf). [source:swissprot;acc:p38117]	Squared	Subtracted	31189.6	37352.8	6163.2	
374	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [source:refseq;acc:nm_004839]	Measured	Subtracted	4246.95	5208.98	962.03	
374	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [source:swissprot;acc:p36544]	Ranked	Subtracted	248.152	267.226	19.074	
374	serine protease htra1 precursor (ec 3.4.21.-) (l56). [source:swissprot;acc:q92743]	Measured	Divided	5066.93	5925.38	1.16942	
374	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [source:swissprot;acc:q9nrc6]	Squared	Divided	45987	56777.1	1.23463	
374	transcription factor dp-2 (e2f dimerization partner 2). [source:swissprot;acc:q14188]	Ranked	Divided	267.208	244.168	1.09436	
375	45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [source:swissprot;acc:q9brk5]	Squared	Divided	45987	56777.1	1.23463	
375	60s ribosomal protein l35. [source:swissprot;acc:p42766]	Rooted	Divided	50.2545	45.5637	1.10295	
375	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [source:swissprot;acc:o43306]	Ranked	Subtracted	248.152	267.226	19.074	
375	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [source:swissprot;acc:o14802]	Ranked	Divided	242.686	265.516	1.09407	
375	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [source:swissprot;acc:q14498]	Rooted	Subtracted	56.3935	62.8817	6.4882	
375	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [source:swissprot;acc:o15116]	Measured	Divided	4700.42	5492.63	1.16854	
375	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [source:swissprot;acc:q99807]	Measured	Subtracted	4250.14	5211.25	961.11	
375	ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [source:refseq;acc:nm_003349]	Squared	Subtracted	29547.4	35683.5	6136.1	

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/