Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Gene description Rank Network Comparison Type Value Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 2408 to 2457 of 3228 in total 
Network Comparison Type	Divided
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

description	Rank	red	green	network_comparison	
ring finger protein 3. [source:refseq;acc:nm_006315]	2763	0.00001	0.00001	1	
ring finger protein 38. [source:refseq;acc:nm_022781]	1652	219.062	215.942	1.01445	
ring finger protein 4. [source:swissprot;acc:p78317]	3189	0.00001	0.00001	1	
ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [source:refseq;acc:nm_014771]	2389	224.414	225.289	1.0039	
ring finger protein 44. [source:refseq;acc:nm_014901]	1650	219.062	215.942	1.01445	
rio kinase 1 isoform 1; ad034 protein. [source:refseq;acc:nm_031480]	921	236.741	245.547	1.0372	
rna (guanine-7-) methyltransferase. [source:refseq;acc:nm_003799]	1912	217.48	215.256	1.01033	
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [source:refseq;acc:nm_007372]	2284	219.652	218.482	1.00536	
rna polymerase i associated factor 53. [source:refseq;acc:nm_022490]	409	241.045	261.874	1.08641	
rna polymerase i transcription factor rrn3. [source:refseq;acc:nm_018427]	2211	199.129	200.413	1.00645	
rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [source:swissprot;acc:o94763]	2371	218.555	219.434	1.00402	
rna, u transporter 1; snurportin-1. [source:refseq;acc:nm_005701]	2091	211.679	210.052	1.00775	
rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [source: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). [source:swissprot;acc:p52756]	1539	228.419	232.376	1.01732	
rna-binding protein 8a (rna binding motif protein 8a) (ribonucleoprotein rbm8a) (rna-binding protein y14) (binder of ovca1- 1) (bov-1). [source: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). [source: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). [source:swissprot;acc:p51513]	693	222.554	234.847	1.05524	
rna-binding protein with multiple splicing (rbp-ms). [source:swissprot;acc:q93062]	1949	218.794	216.663	1.00984	
rna-binding protein. [source: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). [source:swissprot;acc:q9h0z9]	1821	218.36	215.874	1.01152	
rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [source: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. [source:refseq;acc:nm_005156]	1381	218.47	213.876	1.02148	
rp42 homolog; squamous cell carcinoma-related oncogene. [source:refseq;acc:nm_020640]	3198	0.00001	0.00001	1	
rrp5 protein homolog (programmed cell death protein 11). [source: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). [source: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). [source: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). [source: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). [source: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). [source:swissprot;acc:q9y230]	2204	219.377	220.8	1.00649	
rw1 protein (fragment). [source:swissprot;acc:q92545]	838	231.734	222.222	1.0428	
rwd domain containing 1; ptd013 protein; cgi-24 protein. [source: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). [source: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). [source: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). [source:swissprot;acc:p34991]	208	285.684	252.234	1.13261	
saccharomyces cerevisiae nip7p homolog. [source:refseq;acc:nm_016101]	477	251.926	234.547	1.0741	
sad1/unc-84 protein-like 1. [source:swissprot;acc:o94901]	148	296.677	247.559	1.19841	
sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [source:swissprot;acc:q9nsc2]	1387	218.47	213.875	1.02148	
sal-like protein 2 (zinc finger protein sall2) (hsal2). [source:swissprot;acc:q9y467]	1377	218.471	213.876	1.02148	
sal-like protein 3 (zinc finger protein sall3) (hsall3). [source:swissprot;acc:q9bxa9]	1378	218.47	213.876	1.02148	
sal-like protein 4 (zinc finger protein sall4). [source:swissprot;acc:q9ujq4]	1388	218.471	213.876	1.02148	
salivary proline-rich protein po (allele k) [contains: peptide p-d] (fragment). [source: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). [source:swissprot;acc:q9y3z3]	3124	0.00001	0.00001	1	
sarcoglycan zeta; zeta-sarcoglycan. [source:refseq;acc:nm_139167]	1176	218.186	212.672	1.02593	
schwannomin interacting protein 1. [source:refseq;acc:nm_014575]	2900	0.00001	0.00001	1	
scratch; scratch 1. [source:refseq;acc:nm_031309]	1873	210.55	208.305	1.01078	
scribble. [source:refseq;acc:nm_015356]	2528	221.782	222.291	1.0023	
scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [source:refseq;acc:nm_020680]	1575	222.585	218.982	1.01645	
sec13-related protein. [source:swissprot;acc:p55735]	1133	218.484	212.675	1.02731	
sec23-interacting protein p125; phospholipase. [source:refseq;acc:nm_007190]	3097	0.00001	0.00001	1	
secreted modular calcium-binding protein 1. [source:refseq;acc:nm_022137]	1644	217.256	214.149	1.01451	

Legend:
- Rank is the rank after comparing the two networks
- 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.
- http://analysis.yellowcouch.org/