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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 858 to 907 of 16578 in total 
Value Type	Ranked
Filtered	1

Rank	Hugo	description	Network Comparison Type	Interaction Map	red	green	network_comparison	
215	EIF4G1	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [source:swissprot;acc:q04637]	Subtracted	High confidence	237.292	212.457	24.835	
215	GRPR	gastrin-releasing peptide receptor (grp-r) (grp-preferring bombesin receptor). [source:swissprot;acc:p30550]	Subtracted	Low confidence	199.671	209.654	9.983	
215	NEGR1	a kindred of iglon. [source:refseq;acc:nm_173808]	Divided	Low confidence	199.671	209.654	1.05	
216	BRS3	bombesin receptor subtype-3 (brs-3). [source:swissprot;acc:p32247]	Subtracted	Low confidence	199.671	209.654	9.983	
216	MYH4	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [source:swissprot;acc:q9y623]	Divided	High confidence	112	126	1.125	
216	NMBR	neuromedin-b receptor (nmb-r) (neuromedin-b-preferring bombesin receptor). [source:swissprot;acc:p28336]	Divided	Low confidence	199.671	209.654	1.05	
216	SNRPD2	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [source:swissprot;acc:p43330]	Subtracted	High confidence	226.471	201.769	24.702	
217	GRPR	gastrin-releasing peptide receptor (grp-r) (grp-preferring bombesin receptor). [source:swissprot;acc:p30550]	Divided	Low confidence	199.671	209.654	1.05	
217	MYH8	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [source:swissprot;acc:p13535]	Divided	High confidence	112	126	1.125	
217	OGT	udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [source:swissprot;acc:o15294]	Subtracted	Low confidence	206.583	196.743	9.84	
217	RPL26	60s ribosomal protein l26. [source:swissprot;acc:q02877]	Subtracted	High confidence	242.326	267.008	24.682	
218	BRS3	bombesin receptor subtype-3 (brs-3). [source:swissprot;acc:p32247]	Divided	Low confidence	199.671	209.654	1.05	
218	LEF1	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [source:swissprot;acc:q9uju2]	Subtracted	Low confidence	208.289	198.538	9.751	
218	MYH2	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	Divided	High confidence	112	126	1.125	
218	RPL35	60s ribosomal protein l35. [source:swissprot;acc:p42766]	Subtracted	High confidence	242.333	266.999	24.666	
219		40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	Subtracted	High confidence	242.339	266.986	24.647	
219	BACH1	transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [source:swissprot;acc:o14867]	Divided	Low confidence	172.647	164.44	1.04991	
219	MYH3	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [source:swissprot;acc:p11055]	Divided	High confidence	112	126	1.125	
219	NFYA	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [source:swissprot;acc:p23511]	Subtracted	Low confidence	214.032	204.284	9.748	
220	MRPL2	mitochondrial ribosomal protein l2. [source:refseq;acc:nm_015950]	Subtracted	High confidence	242.339	266.986	24.647	
220	MYH1	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [source:swissprot;acc:p12882]	Divided	High confidence	112	126	1.125	
220	NFE2L2	nuclear factor erythroid 2 related factor 2 (nf-e2 related factor 2) (nfe2-related factor 2) (nuclear factor, erythroid derived 2, like 2) (hebp1). [source:swissprot;acc:q16236]	Divided	Low confidence	172.647	164.44	1.04991	
220	TLR2	toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [source:swissprot;acc:o60603]	Subtracted	Low confidence	207.926	198.276	9.65	
221		myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [source:swissprot;acc:p12883]	Divided	High confidence	112	126	1.125	
221		ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	Subtracted	Low confidence	189.373	179.829	9.544	
221	BACH2	transcription regulator protein bach2 (btb and cnc homolog 2). [source:swissprot;acc:q9byv9]	Divided	Low confidence	172.647	164.44	1.04991	
221	EIF1B	protein translation factor sui1 homolog gc20. [source:swissprot;acc:o60739]	Subtracted	High confidence	242.627	267.151	24.524	
222		60s ribosomal protein l14 (cag-isl 7). [source:swissprot;acc:p50914]	Subtracted	High confidence	242.153	266.673	24.52	
222	CASK	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [source:swissprot;acc:o14936]	Subtracted	Low confidence	212.056	202.524	9.532	
222	MYH7B	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [source:sptrembl;acc:q9h430]	Divided	High confidence	112	126	1.125	
222	UBE2E1	ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [source:swissprot;acc:p51965]	Divided	Low confidence	203.935	214.089	1.04979	
223	GTF3C3	general transcription factor iiic, polypeptide 3, 102kda; general transcription factor iiic, polypeptide 3 (102kd); transcription factor iiic, 102 kd. [source:refseq;acc:nm_012086]	Divided	Low confidence	217.228	206.926	1.04979	
223	MYH13	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	Divided	High confidence	112	126	1.125	
223	SIM1	single-minded homolog 1. [source:swissprot;acc:p81133]	Subtracted	Low confidence	212.056	202.524	9.532	
223	SRR	serine racemase (ec 5.1.1.-). [source:swissprot;acc:q9gzt4]	Subtracted	High confidence	242.153	266.673	24.52	
224	NFYC	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [source:swissprot;acc:q13952]	Subtracted	Low confidence	209.649	200.129	9.52	
224	RPL34	60s ribosomal protein l34. [source:swissprot;acc:p49207]	Subtracted	High confidence	242.153	266.673	24.52	
224	SLC15A2	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [source:swissprot;acc:q16348]	Divided	High confidence	185.969	165.623	1.12285	
224	UBE2E4P	ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [source:refseq;acc:nm_006357]	Divided	Low confidence	203.933	214.059	1.04965	
225	ANKRD7	ankyrin repeat domain protein 7 (testis-specific protein tsa806). [source:swissprot;acc:q92527]	Subtracted	Low confidence	216.855	207.34	9.515	
225	SEC61A2	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [source:swissprot;acc:q9y2r3]	Subtracted	High confidence	242.153	266.673	24.52	
225	SLC15A1	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [source:swissprot;acc:p46059]	Divided	Low confidence	201.41	191.974	1.04915	
225	SNRPD2	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [source:swissprot;acc:p43330]	Divided	High confidence	226.471	201.769	1.12243	
226	ANKRD19	ba526d8.2 (novel protein similar to kiaa1074). [source:sptrembl;acc:q9h560]	Subtracted	Low confidence	216.845	207.333	9.512	
226	COMP	cartilage oligomeric matrix protein precursor (comp). [source:swissprot;acc:p49747]	Divided	High confidence	239.991	269.238	1.12187	
226	LEF1	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [source:swissprot;acc:q9uju2]	Divided	Low confidence	208.289	198.538	1.04911	
226	SEC61A1	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [source:swissprot;acc:p38378]	Subtracted	High confidence	242.153	266.673	24.52	
227	ANKRD30A	breast cancer antigen ny-br-1. [source:refseq;acc:nm_052997]	Subtracted	Low confidence	216.842	207.332	9.51	
227	METAP1	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [source:swissprot;acc:p53582]	Subtracted	High confidence	244.126	268.604	24.478	
227	TENC1	c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [source:refseq;acc:nm_015319]	Divided	Low confidence	216.404	206.277	1.04909	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/