MK5 Microarray Data

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

Results: HTML CSV LaTeX

Showing element 262 to 311 of 3228 in total

Network Comparison Type  : Divided
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	Hugo	description	network_comparison	red	green
262	HS3ST3B1	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]	1.11394	219.421	196.978
263	HS3ST2	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]
264	DCPS	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]
265	SF3B1	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	1.11241	225.217	202.459
266	SIN3A	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477]	1.11121	241.07	267.88
267	DENR	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]
268	EIF5	eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]	1.10996	271.016	244.167
269	PCYT1A	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585]	1.10763	241.373	267.352
270	FLAD1	fad synthetase. [refseq;acc:nm_025207]
271	no value	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)]. [swissprot;acc:o95340]
272	LGTN	ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214]
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)]. [swissprot;acc:o43252]
274	POR	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435]
275	PCYT1B	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3]
276	SNORA7A	60s ribosomal protein l32. [swissprot;acc:p02433]	1.10716	241.13	266.969
277	no value	40s ribosomal protein s29. [swissprot;acc:p30054]	1.10665	241.849	267.642
278	RPS11	40s ribosomal protein s11. [swissprot;acc:p04643]	1.10642	241.399	267.088
279	RBBP7	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	1.10605	252.644	228.42
280	MTA1	metastasis-associated protein mta1. [swissprot;acc:q13330]	1.10578	252.512	228.356
281	no value	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	1.10557	241.808	267.335
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). [swissprot;acc:q09028]	1.10553	252.39	228.297
283	RPL11	60s ribosomal protein l11. [swissprot;acc:p39026]	1.10552	241.828	267.346
284	BCAR1	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]	1.10541	224.657	203.235
285	CCT4	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	1.10532	224.647	203.242
286	NEDD9	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511]	1.1052	224.633	203.251
287	RPS4Y2	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	1.10517	240.758	266.079
288	no value	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]			266.078
289		hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	1.10486	272.781	246.892
290	RRM2	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	1.10428	231.969	210.064
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). [swissprot;acc:p25208]	1.10368	251.679	228.037
292	RPS15A	40s ribosomal protein s15a. [swissprot;acc:p39027]	1.10357	241.411	266.414
293	no value	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	1.10356	240.782	265.717
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. [refseq;acc:nm_016567]
295	SCYE1	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]	1.103	223.273	202.423
296	MRPL4	mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956]	1.10294	241.282	266.12
297	no value	60s ribosomal protein l7. [swissprot;acc:p18124]	1.1029	235.727	259.984
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). [swissprot;acc:p17655]	1.10281	268.632	243.588
299	CAPN1	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]		268.635	243.592
300	PITRM1	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	1.10196	150.959	166.351
301	ALG1	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	1.10193	150.982	166.372
302	RPL26	60s ribosomal protein l26. [swissprot;acc:q02877]	1.10185	242.326	267.008
303	RPL35	60s ribosomal protein l35. [swissprot;acc:p42766]	1.10179	242.333	266.999
304	no value	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	1.1017	242.339	266.986
305	MRPL2	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]
306	no value	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	1.10126	242.153	266.673
307	SRR	serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]
308	RPL34	60s ribosomal protein l34. [swissprot;acc:p49207]
309	SEC61A2	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3]
310	SEC61A1	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378]
311	EIF1B	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	1.10108	242.627	267.151

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.