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

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Showing element 2401 to 2450 of 3228 in total

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

description	Rank	red	green	network_comparison
ribosomal protein s6 kinase alpha 6 (ec 2.7.1.37) (s6k-alpha 6) (90 kda ribosomal protein s6 kinase 6) (p90-rsk 6) (ribosomal s6 kinase 4) (rsk-4) (pp90rsk4). [swissprot;acc:q9uk32]	2170	215.925	214.481	1.00673
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	371	186.52	170.42	1.09447
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	372
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050]	2017	127.397	128.553	1.00907
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]	2262	221.599	220.351	1.00566
ring finger protein 20. [refseq;acc:nm_019592]	2388	224.414	225.289	1.0039
ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1]	1588	177.834	180.725	1.01626
ring finger protein 3. [refseq;acc:nm_006315]	2763	0.00001	0.00001	1
ring finger protein 38. [refseq;acc:nm_022781]	1652	219.062	215.942	1.01445
ring finger protein 4. [swissprot;acc:p78317]	3189	0.00001	0.00001	1
ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [refseq;acc:nm_014771]	2389	224.414	225.289	1.0039
ring finger protein 44. [refseq;acc:nm_014901]	1650	219.062	215.942	1.01445
rio kinase 1 isoform 1; ad034 protein. [refseq;acc:nm_031480]	921	236.741	245.547	1.0372
rna (guanine-7-) methyltransferase. [refseq;acc:nm_003799]	1912	217.48	215.256	1.01033
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	2284	219.652	218.482	1.00536
rna polymerase i associated factor 53. [refseq;acc:nm_022490]	409	241.045	261.874	1.08641
rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427]	2211	199.129	200.413	1.00645
rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763]	2371	218.555	219.434	1.00402
rna, u transporter 1; snurportin-1. [refseq;acc:nm_005701]	2091	211.679	210.052	1.00775
rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175]	1532	228.419	232.376	1.01732
rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756]	1539
rna-binding protein 8a (rna binding motif protein 8a) (ribonucleoprotein rbm8a) (rna-binding protein y14) (binder of ovca1- 1) (bov-1). [swissprot;acc:q9y5s9]	2996	0.00001	0.00001	1
rna-binding protein 9 (rna binding motif protein 9) (hexaribonucleotide binding protein 2) (repressor of tamoxifen transcriptional activity). [swissprot;acc:o43251]	1692	218.515	215.551	1.01375
rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513]	693	222.554	234.847	1.05524
rna-binding protein with multiple splicing (rbp-ms). [swissprot;acc:q93062]	1949	218.794	216.663	1.00984
rna-binding protein. [refseq;acc:nm_019027]	247	237.302	212.41	1.11719
rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9]	1821	218.36	215.874	1.01152
rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]	383	237.862	217.739	1.09242
rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [refseq;acc:nm_005156]	1381	218.47	213.876	1.02148
rp42 homolog; squamous cell carcinoma-related oncogene. [refseq;acc:nm_020640]	3198	0.00001	0.00001	1
rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690]	1624	230.643	227.194	1.01518
runt-related transcription factor 1 (core-binding factor, alpha 2 subunit) (cbf-alpha 2) (acute myeloid leukemia 1 protein) (oncogene aml-1) (polyomavirus enhancer binding protein 2 alpha b subunit) (pebp2-alpha b) (pea2-alpha b) (sl3-3 enhancer factor 1 alpha b subunit) (sl3/akv core-binding factor alpha b subunit). [swissprot;acc:q01196]	2877	0.00001	0.00001	1
runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950]	483	237.109	254.667	1.07405
runt-related transcription factor 3 (core-binding factor, alpha 3 subunit) (cbf-alpha 3) (acute myeloid leukemia 2 protein) (oncogene aml-2) (polyomavirus enhancer binding protein 2 alpha c subunit) (pebp2-alpha c) (pea2-alpha c) (sl3-3 enhancer factor 1 alpha c subunit) (sl3/akv core-binding factor alpha c subunit). [swissprot;acc:q13761]	3208	0.00001	0.00001	1
ruvb-like 1 (ec 3.6.1.-) (49-kda tata box-binding protein-interacting protein) (49 kda tbp-interacting protein) (tip49a) (pontin 52) (nuclear matrix protein 238) (nmp 238) (54 kda erythrocyte cytosolic protein) (ecp-54) (tip60-associated protein 54-alpha) (tap54-alpha). [swissprot;acc:q9y265]	1759	219.37	222.086	1.01238
ruvb-like 2 (ec 3.6.1.-) (48-kda tata box-binding protein-interacting protein) (48-kda tbp-interacting protein) (tip49b) (repressing pontin 52) (reptin 52) (51 kda erythrocyte cytosolic protein) (ecp-51) (tip60-associated protein 54-beta) (tap54-beta) (cgi-46). [swissprot;acc:q9y230]	2204	219.377	220.8	1.00649
rw1 protein (fragment). [swissprot;acc:q92545]	838	231.734	222.222	1.0428
rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]	3073	0.00001	0.00001	1
s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266]	2647	212.496	212.25	1.00116
s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153]	2555	212.953	212.572	1.00179
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991]	208	285.684	252.234	1.13261
saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101]	477	251.926	234.547	1.0741
sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	148	296.677	247.559	1.19841
sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [swissprot;acc:q9nsc2]	1387	218.47	213.875	1.02148
sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467]	1377	218.471	213.876
sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9]	1378	218.47
sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4]	1388	218.471
salivary proline-rich protein po (allele k) [contains: peptide p-d] (fragment). [swissprot;acc:p10162]	2716	216.018	215.903	1.00053
sam domain and hd domain-containing protein 1 (dendritic cell-derived ifng-induced protein) (dcip) (monocyte protein 5) (mop-5). [swissprot;acc:q9y3z3]	3124	0.00001	0.00001	1
sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167]	1176	218.186	212.672	1.02593

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.