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

Results: HTML CSV LaTeX

Showing element 358 to 407 of 3228 in total

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

description	Rank	network_comparison	red	green
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	1.02752	218.528	212.676
atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259]	1384	1.02148	218.471	213.876
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	1.03157	221.682	228.68
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	1	0.00001	0.00001
autoantigen ngp-1. [swissprot;acc:q13823]	670	1.05694	250.302	236.817
autophagy protein 12-like (apg12-like). [swissprot;acc:o94817]	1729	1.01304	187.582	190.028
autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]	1540	1.01721	240.077	236.015
axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645]	2003	1.00923	208.315	206.41
b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844]	1559	1.01655	196.191	192.996
b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749]	2655	1.0011	201.445	201.667
b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182]	1556	1.01656	196.192	192.996
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	1.03396	130.289	134.713
b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]	181	1.16294	229.818	267.265
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]	244	1.11785	227.357	254.15
ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]	464	1.07686	210.578	226.764
ba203i16.1 (hypothetical protein kiaa0970). [sptrembl;acc:q9h1w1]	3117	1	0.00001	0.00001
ba207c16.2 (fragment). [sptrembl;acc:q9nql7]	2599	1.00142	211.662	211.361
ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	2148	1.00686	217.871	219.366
ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2]	2115	1.007	214.632	213.14
ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	931	1.03637	159.13	164.917
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	452	1.07784	224.161	207.972
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	1568	1.01646	221.128	224.767
ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [sptrembl;acc:q9bx39]	2968	1	0.00001	0.00001
bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213]	757	1.04968	224.434	235.583
baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]	2500	1.00275	218.949	219.552
bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933]	2185	1.00663	211.713	210.318
bag-family molecular chaperone regulator-2. [swissprot;acc:o95816]	1785	1.01206	206.332	203.874
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	1.07748	233.529	216.737
bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742]	1015	1.03236	221.73	228.906
bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]	651	1.05877	233.725	220.751
band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0]	2144	1.00688	206.443	207.864
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	1.01646	221.128	224.767
barrier-to-autointegration factor (breakpoint cluster region protein 1). [swissprot;acc:o75531]	2804	1	0.00001	0.00001
basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414]	933	1.03635	159.165	164.951
basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	2715	1.00053	216.018	215.903
bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [swissprot;acc:p55061]	2950	1	0.00001	0.00001
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	1.01479	202.358	199.408
bet3 homolog. [swissprot;acc:o43617]	567	1.06563	129.219	121.261
beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612]	1945	1.00987	224.343	222.151
beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929]	2361	1.00415	207.186	208.046
beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	301	1.10193	150.982	166.372
beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [swissprot;acc:q13884]	2576	1.00154	213.422	213.75
beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425]	2578
beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	50	1.26667	133	105
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	49
beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429]	2222	1.00637	221.509	220.108
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	2221

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.