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 Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1601 to 1650 of 14920 in total 
Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
201	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [source:sptrembl;acc:q9nu36]	Squared	0	351.996	499.177	1.41813	
201	calsyntenin-2 precursor. [source:swissprot;acc:q9h4d0]	Squared	1	71033.4	95440.2	1.3436	
201	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [source:swissprot;acc:p39656]	Rooted	1	61.2893	70.3856	1.14842	
201	keratin associated protein 4-14; keratin associated protein 4.14. [source:refseq;acc:nm_033059]	Rooted	0	23.8722	20.9336	1.14038	
201	maspin precursor (protease inhibitor 5). [source:swissprot;acc:p36952]	Ranked	0	16853	15123	1.1144	
201	splicing factor 4 isoform b; rna-binding protein. [source:refseq;acc:nm_021164]	Ranked	1	240.133	211.382	1.13601	
201	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [source:swissprot;acc:q96gm5]	Measured	0	6804.88	5690.63	1.1958	
201	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [source:swissprot;acc:p50991]	Measured	1	4810.22	6075.04	1.26294	
202	calsyntenin-3 precursor. [source:swissprot;acc:q9bqt9]	Squared	1	71030.1	95434.8	1.34358	
202	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [source:swissprot;acc:q9bzj0]	Measured	0	606.049	723.75	1.19421	
202	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [source:swissprot;acc:p42658]	Squared	0	3339.18	2360.97	1.41433	
202	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [source:swissprot;acc:q14511]	Measured	1	4812.01	6076.09	1.26269	
202	keratin associated protein 4.9 (fragment). [source:sptrembl;acc:q9byq8]	Rooted	0	23.8722	20.9336	1.14038	
202	serpin b11. [source:swissprot;acc:q96p15]	Ranked	0	16853	15123	1.1144	
202	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [source:swissprot;acc:q9ubn4]	Ranked	1	201.478	228.784	1.13553	
202	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [source:swissprot;acc:q15393]	Rooted	1	57.3527	65.7973	1.14724	
203	autophagy protein 12-like (apg12-like). [source:swissprot;acc:o94817]	Measured	1	11757.8	9352.11	1.25723	
203	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [source:swissprot;acc:p50452]	Ranked	0	16853	15123	1.1144	
203	ebp50-pdz interactor of 64 kda (epi64 protein). [source:swissprot;acc:q9bxi6]	Ranked	1	201.515	228.752	1.13516	
203	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [source:swissprot;acc:q9y3k8]	Squared	0	93.5732	66.2405	1.41263	
203	hpaii tiny  fragments locus 9c. [source:refseq;acc:nm_022727]	Squared	1	20988.2	15632.1	1.34263	
203	microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [source:refseq;acc:nm_015650]	Measured	0	304	363	1.19408	
203	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [source:swissprot;acc:o75642]	Rooted	0	22.1344	25.2414	1.14037	
203	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [source:swissprot;acc:q14186]	Rooted	1	46.3291	53.1063	1.14628	
204	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [source:refseq;acc:nm_017743]	Ranked	0	15081.8	16802.1	1.11406	
204	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [source:swissprot;acc:p50150]	Squared	0	94.1723	66.6659	1.4126	
204	keratin associated protein 4-12; keratin associated protein 4.12. [source:refseq;acc:nm_031854]	Rooted	0	23.8722	20.9337	1.14037	
204	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [source:swissprot;acc:q9ul62]	Ranked	1	201.515	228.752	1.13516	
204	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [source:swissprot;acc:p08578]	Measured	1	4512.19	5655.52	1.25339	
204	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [source:swissprot;acc:p08578]	Rooted	1	55.8956	63.9636	1.14434	
204	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [source:refseq;acc:nm_178862]	Squared	1	12326.4	16522.9	1.34045	
204	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [source:swissprot;acc:p55855]	Measured	0	7981.68	6685.11	1.19395	
205	60s ribosomal protein l23a. [source:swissprot;acc:p29316]	Ranked	0	11844.9	10636.3	1.11363	
205	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	Ranked	1	228.1	200.968	1.13501	
205	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	Squared	1	12326.4	16522.9	1.34045	
205	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [source:swissprot;acc:q15356]	Measured	1	4512.19	5655.52	1.25339	
205	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [source:swissprot;acc:q15356]	Rooted	1	55.8956	63.9636	1.14434	
205	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [source:swissprot;acc:q9nrc6]	Measured	0	5418.2	4543.75	1.19245	
205	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [source:swissprot;acc:p59095]	Rooted	0	23.8722	20.9337	1.14037	
205	t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [source:swissprot;acc:p40227]	Squared	0	99.0201	139.876	1.4126	
206	atlastin; guanylate-binding protein 3. [source:refseq;acc:nm_015915]	Measured	1	5720.25	4577.5	1.24965	
206	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [source:swissprot;acc:p39656]	Squared	1	12326.4	16522.9	1.34045	
206	espin. [source:refseq;acc:nm_031475]	Rooted	0	23.8722	20.934	1.14036	
206	gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]	Rooted	1	140.508	122.878	1.14348	
206	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [source:refseq;acc:nm_023934]	Ranked	0	7479	6716	1.11361	
206	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	Ranked	1	228.085	201.006	1.13472	
206	pms1 protein homolog 2 (dna mismatch repair protein pms2). [source:swissprot;acc:p54278]	Measured	0	1124.15	943.423	1.19157	
206	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [source:swissprot;acc:p14678]	Squared	0	8.27667	5.86733	1.41064	
207	apg3p; pc3-96 protein. [source:refseq;acc:nm_022488]	Rooted	1	140.508	122.878	1.14348	
207	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [source:refseq;acc:nm_002973]	Squared	0	73080.8	102814	1.40685	

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/