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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

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

Results: HTML CSV LaTeX

Showing element 530 to 579 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Hugo	Network Comparison Type	red	network_comparison	green
265	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	SF3B1	Divided	225.217	1.11241	202.459
266	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	RPL10L	Subtracted	243.12	23.542	266.662
	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477]	SIN3A	Divided	241.07	1.11121	267.88
267	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	no value	Subtracted	243.12	23.541	266.661
	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]	DENR	Divided	241.07	1.11121	267.88
268	eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]	EIF5		271.016	1.10996	244.167
	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	PRMT3	Subtracted	241.625	23.511	265.136
269	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	no value
	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585]	PCYT1A	Divided	241.373	1.10763	267.352
270	40s ribosomal protein s3. [swissprot;acc:p23396]	RPS3	Subtracted	241.612	23.507	265.119
	fad synthetase. [refseq;acc:nm_025207]	FLAD1	Divided	241.373	1.10763	267.352
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)]. [swissprot;acc:o95340]	no value
	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	SEC61G	Subtracted	243.072	23.487	266.559
272	ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214]	LGTN	Divided	241.373	1.10763	267.352
	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	MRPL17	Subtracted	242.83	23.418	266.248
273	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]	PAPSS1	Divided	241.373	1.10763	267.352
	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876]	POLR2B	Subtracted	243.208	23.409	266.617
274	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	MRPL36		242.744	23.326	266.07
	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435]	POR	Divided	241.373	1.10763	267.352
275	40s ribosomal protein s5. [swissprot;acc:p46782]	RPS5	Subtracted	242.473	23.283	265.756
	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3]	PCYT1B	Divided	241.373	1.10763	267.352
276	60s ribosomal protein l32. [swissprot;acc:p02433]	SNORA7A		241.13	1.10716	266.969
	atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]	DDX24	Subtracted	258.437	23.254	235.183
277	40s ribosomal protein s29. [swissprot;acc:p30054]	no value	Divided	241.849	1.10665	267.642
	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]	RPL4	Subtracted	239.277	23.157	262.434
278	40s ribosomal protein s11. [swissprot;acc:p04643]	RPS11	Divided	241.399	1.10642	267.088
	myelin gene expression factor 2. [refseq;acc:nm_016132]	MYEF2	Subtracted	235.383	23.093	258.476
279	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	RBBP7	Divided	252.644	1.10605	228.42
	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	PUS1	Subtracted	242.66	23.055	265.715
280	metastasis-associated protein mta1. [swissprot;acc:q13330]	MTA1	Divided	252.512	1.10578	228.356
	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	TFDP2	Subtracted	267.208	23.04	244.168
281	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]	MRPL12		242.159	22.945	265.104
	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	no value	Divided	241.808	1.10557	267.335
282	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]	RBBP4		252.39	1.10553	228.297
	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]	NUDT12	Subtracted	242.159	22.945	265.104
283	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7]	MRPL11		242.37	22.885	265.255
	60s ribosomal protein l11. [swissprot;acc:p39026]	RPL11	Divided	241.828	1.10552	267.346
284	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]	BCAR1		224.657	1.10541	203.235
	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802]	POLR3A	Subtracted	242.686	22.83	265.516
285	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602]	POLR1A		242.691	22.79	265.481
	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	CCT4	Divided	224.647	1.10532	203.242
286	60s ribosomal protein l30. [swissprot;acc:p04645]	RPL30	Subtracted	242.593	22.772	265.365
	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]	NEDD9	Divided	224.633	1.1052	203.251
287	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	RPS4Y2		240.758	1.10517	266.079
	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	SF3B1	Subtracted	225.217	22.758	202.459
288	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	no value	Divided	240.758	1.10517	266.078
	syntaxin 10 (syn10). [swissprot;acc:o60499]	STX10	Subtracted	234.691	22.751	257.442
289	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	no value	Divided	272.781	1.10486	246.892
	syntaxin 6. [swissprot;acc:o43752]	STX6	Subtracted	234.673	22.741	257.414
290	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	RRM2	Divided	231.969	1.10428	210.064

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.