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 Filtered Value Type Network Comparison Type Interaction Map red network_comparison green
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
red
network_comparison
green
blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] 183 0 375.07 1.22281 306.727
2271 1 6568.51 1.04589 6869.97
bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 453 0 1337.29 1.01438 1356.52
861 1 5734.15 1.10329 6326.41
bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] 2406 5078.5 1.03884 5275.76
bone morphogenetic protein 5 precursor (bmp-5). [swissprot;acc:p22003] 3069 0.00001 1 0.00001
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 0 501.151 1.71473 859.34
2773 1 0.00001 1 0.00001
brachyury protein (t protein). [swissprot;acc:o15178] 1631 6179.59 1.07016 6613.15
brain protein 16. [refseq;acc:nm_016458] 274 0 2155.75 1.12172 2418.14
1923 1 5774.02 1.06217 6133.01
brain protein 44. [swissprot;acc:o95563] 328 15999.1 1.18801 19007.1
branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] 1213 5890.62 1.08588 6396.53
branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] 1215 5892.05 1.08575 6397.28
brca1 associated protein. [refseq;acc:nm_006768] 502 0 0.00001 1 0.00001
3161 1
brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] 1939 5669.9 1.061 6015.75
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 3672.49 1.0546 3482.34
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 173 4579.34 1.29727 5940.64
breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] 2442 5454.62 1.0336 5637.88
breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 418 5493.1 1.15603 6350.19
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 5628.53 1.0773 6063.61
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 6252.27 1.15038 7192.51
bromodomain and phd finger-containing protein 3 (fragment). [swissprot;acc:q9uld4] 3149 0.00001 1 0.00001
bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [refseq;acc:nm_013263] 1925 7260.23 1.06213 7711.29
bromodomain-containing protein 1 (br140-like protein). [swissprot;acc:o95696] 3139 0.00001 1 0.00001
bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] 1892 5438.52 1.06334 5783.01
bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] 1891 5438.18 5782.62
bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885] 1888 5438.6 1.06335 5783.11
bs4 protein (ny-ren-18 antigen). [swissprot;acc:q9y5a7] 3214 0.00001 1 0.00001
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 4608.91 1.00702 4576.78
bup protein. [refseq;acc:nm_012071] 2911 0.00001 1 0.00001
bystin. [swissprot;acc:q13895] 343 0 2930.88 1.0699 3135.76
950 1 4280.99 1.09718 4697.02
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 4860.34 1.05493 5127.3
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 5941.24 1.06001 6297.78
c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 1638 9895.77 1.07002 9248.18
c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 1630 9903.22 1.07018 9253.79
c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 488 10872.4 1.14483 12447
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 5869.97 1.07347 6301.24
c18b11 homolog (44.9kd). [refseq;acc:nm_152260] 707 5317.78 1.11781 5944.25
c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] 2120 6951.29 1.05434 7329
c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 261 0 1295.81 1.12945 1463.55
2174 1 3641.45 1.05152 3463.02
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 2421 7355.46 1.0376 7088.93
ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] 874 9921.43 1.10278 10941.2
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 4970.21 1.09761 5455.34

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/