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

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 Rank Gene Value Type Filtered green Network Comparison Type red Interaction Map network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 3730 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
description
Rank
Filtered
green
red
network_comparison
blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] 183 0 306.727 375.07 1.22281
2271 1 6869.97 6568.51 1.04589
bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 453 0 1356.52 1337.29 1.01438
861 1 6326.41 5734.15 1.10329
bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] 2406 5275.76 5078.5 1.03884
bone morphogenetic protein 5 precursor (bmp-5). [swissprot;acc:p22003] 3069 0.00001 0.00001 1
bone morphogenetic protein 6 precursor (bmp-6). [swissprot;acc:p22004] 2896
bone morphogenetic protein 7 precursor (bmp-7) (osteogenic protein 1) (op-1). [swissprot;acc:p18075] 3128
bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] 74 0 859.34 501.151 1.71473
2773 1 0.00001 0.00001 1
brachyury protein (t protein). [swissprot;acc:o15178] 1631 6613.15 6179.59 1.07016
brain protein 16. [refseq;acc:nm_016458] 274 0 2418.14 2155.75 1.12172
1923 1 6133.01 5774.02 1.06217
brain protein 44. [swissprot;acc:o95563] 328 19007.1 15999.1 1.18801
branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] 1213 6396.53 5890.62 1.08588
branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] 1215 6397.28 5892.05 1.08575
brca1 associated protein. [refseq;acc:nm_006768] 502 0 0.00001 0.00001 1
3161 1
brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] 1939 6015.75 5669.9 1.061
brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] 2116 3482.34 3672.49 1.0546
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 173 5940.64 4579.34 1.29727
breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] 2442 5637.88 5454.62 1.0336
breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 418 6350.19 5493.1 1.15603
brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [swissprot;acc:q9y6d6] 1425 6063.61 5628.53 1.0773
brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] 1423
brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 443 7192.51 6252.27 1.15038
bromodomain and phd finger-containing protein 3 (fragment). [swissprot;acc:q9uld4] 3149 0.00001 0.00001 1
bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [refseq;acc:nm_013263] 1925 7711.29 7260.23 1.06213
bromodomain-containing protein 1 (br140-like protein). [swissprot;acc:o95696] 3139 0.00001 0.00001 1
bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] 1892 5783.01 5438.52 1.06334
bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] 1891 5782.62 5438.18
bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885] 1888 5783.11 5438.6 1.06335
bs4 protein (ny-ren-18 antigen). [swissprot;acc:q9y5a7] 3214 0.00001 0.00001 1
bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] 2664 4576.78 4608.91 1.00702
bup protein. [refseq;acc:nm_012071] 2911 0.00001 0.00001 1
bystin. [swissprot;acc:q13895] 343 0 3135.76 2930.88 1.0699
950 1 4697.02 4280.99 1.09718
c-1-tetrahydrofolate synthase, cytoplasmic (c1-thf synthase) [includes: methylenetetrahydrofolate dehydrogenase (ec 1.5.1.5); methenyltetrahydrofolate cyclohydrolase (ec 3.5.4.9); formyltetrahydrofolate synthetase (ec 6.3.4.3)]. [swissprot;acc:p11586] 2102 5127.3 4860.34 1.05493
c-jun-amino-terminal kinase interacting protein 3 (jnk-interacting protein 3) (jip-3) (jnk map kinase scaffold protein 3) (mitogen- activated protein kinase 8-interacting protein 3). [swissprot;acc:q9upt6] 1962 6297.78 5941.24 1.06001
c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 1638 9248.18 9895.77 1.07002
c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 1630 9253.79 9903.22 1.07018
c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 488 12447 10872.4 1.14483
c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319] 1528 6301.24 5869.97 1.07347
c18b11 homolog (44.9kd). [refseq;acc:nm_152260] 707 5944.25 5317.78 1.11781
c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] 2120 7329 6951.29 1.05434
c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 261 0 1463.55 1295.81 1.12945
2174 1 3463.02 3641.45 1.05152
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 2421 7088.93 7355.46 1.0376
ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] 874 10941.2 9921.43 1.10278
caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844] 941 5455.34 4970.21 1.09761

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.
- http://analysis.yellowcouch.org/