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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 258 to 307 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
258	MXD4	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	227.999	204.366	1.11564	
259	RAB24	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	227.999	204.37	1.11562	
260	HS3ST6	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [source:sptrembl;acc:q96qi5]	219.421	196.978	1.11394	
261	HS3ST3A1	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006042]	219.421	196.978	1.11394	
262	HS3ST3B1	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [source:refseq;acc:nm_006041]	219.421	196.978	1.11394	
263	HS3ST2	heparan sulfate d-glucosaminyl  3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006043]	219.421	196.978	1.11394	
264	DCPS	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [source:refseq;acc:nm_014026]	219.421	196.978	1.11394	
265	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]	225.217	202.459	1.11241	
266	SIN3A	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [source:refseq;acc:nm_015477]	241.07	267.88	1.11121	
267	DENR	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [source:swissprot;acc:o43583]	241.07	267.88	1.11121	
268	EIF5	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	271.016	244.167	1.10996	
269	PCYT1A	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [source:swissprot;acc:p49585]	241.373	267.352	1.10763	
270	FLAD1	fad synthetase. [source:refseq;acc:nm_025207]	241.373	267.352	1.10763	
271		bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o95340]	241.373	267.352	1.10763	
272	LGTN	ligatin (hepatocellular carcinoma-associated antigen 56). [source:swissprot;acc:p41214]	241.373	267.352	1.10763	
273	PAPSS1	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o43252]	241.373	267.352	1.10763	
274	POR	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [source:swissprot;acc:p16435]	241.373	267.352	1.10763	
275	PCYT1B	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [source:swissprot;acc:q9y5k3]	241.373	267.352	1.10763	
276	SNORA7A	60s ribosomal protein l32. [source:swissprot;acc:p02433]	241.13	266.969	1.10716	
277		40s ribosomal protein s29. [source:swissprot;acc:p30054]	241.849	267.642	1.10665	
278	RPS11	40s ribosomal protein s11. [source:swissprot;acc:p04643]	241.399	267.088	1.10642	
279	RBBP7	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [source:swissprot;acc:q16576]	252.644	228.42	1.10605	
280	MTA1	metastasis-associated protein mta1. [source:swissprot;acc:q13330]	252.512	228.356	1.10578	
281		60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621]	241.808	267.335	1.10557	
282	RBBP4	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [source:swissprot;acc:q09028]	252.39	228.297	1.10553	
283	RPL11	60s ribosomal protein l11. [source:swissprot;acc:p39026]	241.828	267.346	1.10552	
284	BCAR1	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [source:swissprot;acc:p56945]	224.657	203.235	1.10541	
285	CCT4	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [source:swissprot;acc:p50991]	224.647	203.242	1.10532	
286	NEDD9	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]	224.633	203.251	1.1052	
287	RPS4Y2	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	240.758	266.079	1.10517	
288		40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	240.758	266.078	1.10517	
289		hpaii tiny  fragments locus 9c. [source:refseq;acc:nm_022727]	272.781	246.892	1.10486	
290	RRM2	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [source:swissprot;acc:p31350]	231.969	210.064	1.10428	
291	NFYB	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [source:swissprot;acc:p25208]	251.679	228.037	1.10368	
292	RPS15A	40s ribosomal protein s15a. [source:swissprot;acc:p39027]	241.411	266.414	1.10357	
293		60s ribosomal protein l23 (l17). [source:swissprot;acc:p23131]	240.782	265.717	1.10356	
294	BCCIP	brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [source:refseq;acc:nm_016567]	240.782	265.717	1.10356	
295	SCYE1	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [source:swissprot;acc:q12904]	223.273	202.423	1.103	
296	MRPL4	mitochondrial ribosomal protein l4 isoform a. [source:refseq;acc:nm_015956]	241.282	266.12	1.10294	
297		60s ribosomal protein l7. [source:swissprot;acc:p18124]	235.727	259.984	1.1029	
298	CAPN2	calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [source:swissprot;acc:p17655]	268.632	243.588	1.10281	
299	CAPN1	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [source:swissprot;acc:p07384]	268.635	243.592	1.10281	
300	PITRM1	metalloprotease 1; metalloprotease 1 (pitrilysin family). [source:refseq;acc:nm_014889]	150.959	166.351	1.10196	
301	ALG1	beta-1,4 mannosyltransferase. [source:refseq;acc:nm_019109]	150.982	166.372	1.10193	
302	RPL26	60s ribosomal protein l26. [source:swissprot;acc:q02877]	242.326	267.008	1.10185	
303	RPL35	60s ribosomal protein l35. [source:swissprot;acc:p42766]	242.333	266.999	1.10179	
304		40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	242.339	266.986	1.1017	
305	MRPL2	mitochondrial ribosomal protein l2. [source:refseq;acc:nm_015950]	242.339	266.986	1.1017	
306		60s ribosomal protein l14 (cag-isl 7). [source:swissprot;acc:p50914]	242.153	266.673	1.10126	
307	SRR	serine racemase (ec 5.1.1.-). [source:swissprot;acc:q9gzt4]	242.153	266.673	1.10126	

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/