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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Value Type Interaction Map description Rank Network Comparison Type Gene red green Filtered network_comparison
Results: HTML CSV LaTeX Showing element 2430 to 2479 of 3228 in total 
Value Type	Measured
Interaction Map	High confidence
Network Comparison Type	Divided
Filtered	1

description	Rank	red	green	network_comparison	
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]	1108	4846.16	5283.08	1.09016	
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]	2692	4113.79	4095.53	1.00446	
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]	1895	5882.1	6252.66	1.063	
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]	1899	5786.36	6149.1	1.06269	
rw1 protein (fragment). [source:swissprot;acc:q92545]	390	4533.74	5279.4	1.16447	
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]	1034	6152.88	6732.12	1.09414	
s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [source:swissprot;acc:p31153]	1027	6123.15	6700.05	1.09422	
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]	99	2353.63	3225.65	1.3705	
saccharomyces cerevisiae nip7p homolog. [source:refseq;acc:nm_016101]	425	3729.02	4301.58	1.15354	
sad1/unc-84 protein-like 1. [source:swissprot;acc:o94901]	144	3349.9	4362.61	1.30231	
sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [source:swissprot;acc:q9nsc2]	2286	5783.76	6048.94	1.04585	
sal-like protein 2 (zinc finger protein sall2) (hsal2). [source:swissprot;acc:q9y467]	2276	5783.69	6048.87	1.04585	
sal-like protein 3 (zinc finger protein sall3) (hsall3). [source:swissprot;acc:q9bxa9]	2277	5783.72	6048.9	1.04585	
sal-like protein 4 (zinc finger protein sall4). [source:swissprot;acc:q9ujq4]	2287	5783.7	6048.88	1.04585	
salivary proline-rich protein po (allele k) [contains: peptide p-d] (fragment). [source:swissprot;acc:p10162]	1921	6262.66	6652.85	1.0623	
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]	736	5768.32	6434.78	1.11554	
schwannomin interacting protein 1. [source:refseq;acc:nm_014575]	2900	0.00001	0.00001	1	
scratch; scratch 1. [source:refseq;acc:nm_031309]	918	7281.6	8001.64	1.09888	
scribble. [source:refseq;acc:nm_015356]	1985	5516.89	5844.37	1.05936	
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]	1058	5412.23	5913.4	1.0926	
sec13-related protein. [source:swissprot;acc:p55735]	772	5874.76	6533.36	1.11211	
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]	1553	5875.75	6302.76	1.07267	
secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [source:refseq;acc:nm_022138]	1555	5875.75	6302.76	1.07267	
secretory carrier-associated membrane protein 1. [source:swissprot;acc:o15126]	1082	6439.35	7031.8	1.092	
secretory carrier-associated membrane protein 2. [source:swissprot;acc:o15127]	1080	6439.3	7031.73	1.092	
secretory carrier-associated membrane protein 3. [source:swissprot;acc:o14828]	1081	6439.3	7031.73	1.092	
secretory pathway component sec31b-1. [source:refseq;acc:nm_015490]	781	5874.76	6533.36	1.11211	
sedlin. [source:swissprot;acc:o14582]	350	17396.9	20483.9	1.17745	
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [source:swissprot;acc:o14640]	308	4977.09	5966.44	1.19878	
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [source:swissprot;acc:o14641]	309	4977.8	5966.14	1.19855	
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [source:swissprot;acc:q92997]	311	4981.52	5964.58	1.19734	
selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [source:swissprot;acc:p49903]	558	6167.93	7007.7	1.13615	
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [source:swissprot;acc:q99611]	555	6167.93	7007.7	1.13615	
semaphorin 6b precursor (semaphorin z) (sema z). [source:swissprot;acc:q9h3t3]	2832	0.00001	0.00001	1	
semaphorin 6c precursor (semaphorin y) (sema y). [source:swissprot;acc:q9h3t2]	2933	0.00001	0.00001	1	
semaphorin 6d isoform 3 precursor. [source:refseq;acc:nm_153617]	2964	0.00001	0.00001	1	
senescence marker protein-30 (smp-30) (regucalcin) (rc). [source:swissprot;acc:q15493]	2687	3953.53	3972.32	1.00475	
sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [source:swissprot;acc:q96ld8]	2843	0.00001	0.00001	1	
seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [source:swissprot;acc:q12884]	931	5638.59	6194.17	1.09853	
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [source:swissprot;acc:q8wyj6]	346	14229.2	16780.7	1.17931	
septin 10 isoform 1. [source:refseq;acc:nm_144710]	327	16067.4	19094.4	1.18839	
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [source:swissprot;acc:o43236]	334	14924.4	17655.2	1.18298	
septin 6. [source:swissprot;acc:q14141]	330	15959.9	18957.1	1.1878	
septin 7 (cdc10 protein homolog). [source:swissprot;acc:q16181]	329	15999.1	19007.1	1.18801	

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/