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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 1208 to 1257 of 16578 in total

Value Type	Ranked
Filtered	1

Rank	Hugo	description	Network Comparison Type	Interaction Map	red	green	network_comparison	
302	XPR1	xenotropic and polytropic retrovirus receptor. [source:refseq;acc:nm_004736]	Divided	Low confidence	209.12	200.548	1.04274	
303		melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [source:swissprot;acc:p43357]	Subtracted	High confidence	88.2482	110.265	22.0168	
303	HOMER3	homer, neuronal immediate early gene, 3. [source:refseq;acc:nm_004838]	Divided	Low confidence	210.057	201.45	1.04273	
303	KCNA1	potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [source:swissprot;acc:q09470]	Subtracted	Low confidence	209.58	201.251	8.329	
303	RPL35	60s ribosomal protein l35. [source:swissprot;acc:p42766]	Divided	High confidence	242.333	266.999	1.10179	
304		40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	Divided	High confidence	242.339	266.986	1.1017	
304	KCNA4	potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [source:swissprot;acc:p22459]	Subtracted	Low confidence	209.579	201.251	8.328	
304	KHDRBS1	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [source:refseq;acc:nm_006559]	Divided	Low confidence	209.232	200.662	1.04271	
304	MAGEA11	melanoma-associated antigen 11 (mage-11 antigen). [source:swissprot;acc:p43364]	Subtracted	High confidence	88.2482	110.265	22.0168	
305	HOMER1	homer, neuronal immediate early gene, 1b. [source:refseq;acc:nm_004272]	Divided	Low confidence	210.05	201.454	1.04267	
305	MAGEA2B	melanoma-associated antigen 2 (mage-2 antigen). [source:swissprot;acc:p43356]	Subtracted	High confidence	88.2482	110.265	22.0168	
305	MRPL2	mitochondrial ribosomal protein l2. [source:refseq;acc:nm_015950]	Divided	High confidence	242.339	266.986	1.1017	
305	SNRPD1	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [source:swissprot;acc:p13641]	Subtracted	Low confidence	200.288	192.004	8.284	
306		60s ribosomal protein l14 (cag-isl 7). [source:swissprot;acc:p50914]	Divided	High confidence	242.153	266.673	1.10126	
306		hepatocellular carcinoma-associated protein hca1. [source:refseq;acc:nm_020932]	Subtracted	High confidence	88.2482	110.265	22.0168	
306	NUDT21	cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [source:refseq;acc:nm_007006]	Subtracted	Low confidence	212.262	203.991	8.271	
306	SNRPF	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [source:swissprot;acc:q15356]	Divided	Low confidence	202.122	193.867	1.04258	
307	ITGB1BP2	integrin beta-1 binding protein 2 (melusin) (mstp015). [source:swissprot;acc:q9ukp3]	Subtracted	Low confidence	212.262	203.991	8.271	
307	MAGEA6	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [source:swissprot;acc:p43360]	Subtracted	High confidence	88.2482	110.265	22.0168	
307	PHKG1	phosphorylase b kinase gamma catalytic chain, skeletal muscle isoform (ec 2.7.1.38) (phosphorylase kinase gamma subunit 1). [source:swissprot;acc:q16816]	Divided	Low confidence	217.957	227.209	1.04245	
307	SRR	serine racemase (ec 5.1.1.-). [source:swissprot;acc:q9gzt4]	Divided	High confidence	242.153	266.673	1.10126	
308	HOMER2	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [source:refseq;acc:nm_004839]	Divided	Low confidence	210.018	201.475	1.0424	
308	NDN	necdin. [source:swissprot;acc:q99608]	Subtracted	High confidence	88.2482	110.265	22.0168	
308	RAB3GAP2	rab3 gtpase-activating protein, non-catalytic subunit. [source:refseq;acc:nm_012414]	Subtracted	Low confidence	212.262	203.991	8.271	
308	RPL34	60s ribosomal protein l34. [source:swissprot;acc:p49207]	Divided	High confidence	242.153	266.673	1.10126	
309		microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [source:swissprot;acc:p21378]	Divided	Low confidence	200.213	192.103	1.04222	
309	MAGED1	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [source:swissprot;acc:q9y5v3]	Subtracted	High confidence	88.2482	110.265	22.0168	
309	NDUFA9	nadh-ubiquinone oxidoreductase 39 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-39kd) (ci-39kd). [source:swissprot;acc:q16795]	Subtracted	Low confidence	205.75	197.484	8.266	
309	SEC61A2	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [source:swissprot;acc:q9y2r3]	Divided	High confidence	242.153	266.673	1.10126	
310	MAGEF1	melanoma-associated antigen f1 (mage-f1 antigen). [source:swissprot;acc:q9hay2]	Subtracted	High confidence	88.2482	110.265	22.0168	
310	NDUFA9	nadh-ubiquinone oxidoreductase 39 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-39kd) (ci-39kd). [source:swissprot;acc:q16795]	Divided	Low confidence	205.75	197.484	1.04186	
310	SEC61A1	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [source:swissprot;acc:p38378]	Divided	High confidence	242.153	266.673	1.10126	
310	SNRPF	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [source:swissprot;acc:q15356]	Subtracted	Low confidence	202.122	193.867	8.255	
311	EIF1B	protein translation factor sui1 homolog gc20. [source:swissprot;acc:o60739]	Divided	High confidence	242.627	267.151	1.10108	
311	EXOC7	exocyst complex component exo70. [source:swissprot;acc:q9upt5]	Subtracted	Low confidence	204.124	212.339	8.215	
311	MAGEB6B	melanoma antigen, family b, 6. [source:refseq;acc:nm_173523]	Subtracted	High confidence	88.2482	110.265	22.0168	
311	UBE1C	ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [source:refseq;acc:nm_003968]	Divided	Low confidence	192.088	184.374	1.04184	
312		melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [source:swissprot;acc:p43358]	Subtracted	High confidence	88.2482	110.265	22.0168	
312	BACH1	transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [source:swissprot;acc:o14867]	Subtracted	Low confidence	172.647	164.44	8.207	
312	RPL3L	60s ribosomal protein l3-like. [source:swissprot;acc:q92901]	Divided	High confidence	242.195	266.663	1.10103	
312	SNRPA1	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [source:swissprot;acc:p09661]	Divided	Low confidence	202.051	193.937	1.04184	
313		ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [source:sptrembl;acc:q9nu36]	Divided	Low confidence	202.05	193.94	1.04182	
313	MAGEA9	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	Subtracted	High confidence	88.2482	110.265	22.0168	
313	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]	Subtracted	Low confidence	172.647	164.44	8.207	
313	RRM2B	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	Divided	High confidence	232.473	211.207	1.10069	
314	BACH2	transcription regulator protein bach2 (btb and cnc homolog 2). [source:swissprot;acc:q9byv9]	Subtracted	Low confidence	172.647	164.44	8.207	
314	MAGEA8	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	Subtracted	High confidence	88.2482	110.265	22.0168	
314	METAP1	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [source:swissprot;acc:p53582]	Divided	High confidence	244.126	268.604	1.10027	
314	SF3B1	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533]	Divided	Low confidence	202.057	193.952	1.04179	
315	MAGEC1	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	Subtracted	High confidence	88.2482	110.265	22.0168	

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/