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

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Showing element 351 to 400 of 3228 in total

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

description	Rank	red	green	network_comparison
atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762]	1703	216.079	219.024	1.01363
atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	529	251.653	235.506	1.06856
atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]	328	258.437	235.183	1.09888
atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]	428	253.852	234.808	1.0811
atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010]	990	243.297	235.373	1.03367
atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2]	1365	228.644	223.736	1.02194
atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565]	1126	218.487	212.656	1.02742
atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632]	1120	218.528	212.676	1.02752
atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259]	1384	218.471	213.876	1.02148
atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301]	1035	221.682	228.68	1.03157
au rna-binding protein/enoyl-coenzyme a hydratase precursor; au rna-binding protein/enoyl-coenzyme a hydratase; 3-methylglutaconyl-coa hydratase; mga type i. [refseq;acc:nm_001698]	2913	0.00001	0.00001	1
autoantigen ngp-1. [swissprot;acc:q13823]	670	250.302	236.817	1.05694
autophagy protein 12-like (apg12-like). [swissprot;acc:o94817]	1729	187.582	190.028	1.01304
autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]	1540	240.077	236.015	1.01721
axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645]	2003	208.315	206.41	1.00923
b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844]	1559	196.191	192.996	1.01655
b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749]	2655	201.445	201.667	1.0011
b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182]	1556	196.192	192.996	1.01656
b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]	980	130.289	134.713	1.03396
b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]	181	229.818	267.265	1.16294
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]	244	227.357	254.15	1.11785
ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]	464	210.578	226.764	1.07686
ba203i16.1 (hypothetical protein kiaa0970). [sptrembl;acc:q9h1w1]	3117	0.00001	0.00001	1
ba207c16.2 (fragment). [sptrembl;acc:q9nql7]	2599	211.662	211.361	1.00142
ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	2148	217.871	219.366	1.00686
ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2]	2115	214.632	213.14	1.007
ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	931	159.13	164.917	1.03637
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	452	224.161	207.972	1.07784
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	1568	221.128	224.767	1.01646
ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [sptrembl;acc:q9bx39]	2968	0.00001	0.00001	1
bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213]	757	224.434	235.583	1.04968
baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]	2500	218.949	219.552	1.00275
bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933]	2185	211.713	210.318	1.00663
bag-family molecular chaperone regulator-2. [swissprot;acc:o95816]	1785	206.332	203.874	1.01206
bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817]	459	233.529	216.737	1.07748
bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742]	1015	221.73	228.906	1.03236
bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]	651	233.725	220.751	1.05877
band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0]	2144	206.443	207.864	1.00688
band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491]	2146
band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2]	2145	206.442	207.862
bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824]	1567	221.128	224.767	1.01646
barrier-to-autointegration factor (breakpoint cluster region protein 1). [swissprot;acc:o75531]	2804	0.00001	0.00001	1
basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414]	933	159.165	164.951	1.03635
basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	2715	216.018	215.903	1.00053
bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [swissprot;acc:p55061]	2950	0.00001	0.00001	1
bcl-6 interacting corepressor isoform 1. [refseq;acc:nm_017745]	2776
beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457]	1636	202.358	199.408	1.01479
bet3 homolog. [swissprot;acc:o43617]	567	129.219	121.261	1.06563
beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612]	1945	224.343	222.151	1.00987
beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929]	2361	207.186	208.046	1.00415

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
- 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.