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 Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 3730 in total
Value Type  : Ranked
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] 419 0 17183 16684 1.02991
1928 1 198.935 196.964 1.01001
bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 114 0 10603.2 8871.11 1.19525
1748 1 212.971 215.673 1.01269
bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] 793 234.511 224.244 1.04578
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] 91 0 11127.5 13841.2 1.24387
2773 1 0.00001 0.00001 1
brachyury protein (t protein). [swissprot;acc:o15178] 2040 208.803 210.586 1.00854
brain protein 16. [refseq;acc:nm_016458] 49 0 4854.99 6890.54 1.41927
1847 1 219.195 216.811 1.011
brain protein 44. [swissprot;acc:o95563] 742 120.078 126.215 1.05111
branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] 2672 210.741 210.957 1.00102
branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] 2687 210.755 210.939 1.00087
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] 1752 218.991 216.271 1.01258
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] 294 265.717 240.782 1.10356
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 229 202.094 226.401 1.12028
breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] 939 224.27 216.501 1.03588
breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 691 206.195 217.602 1.05532
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] 2713 220.395 220.521 1.00057
brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] 2711
brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 945 205.085 212.44 1.03586
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] 2747 201.514 201.477 1.00018
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] 2241 224.338 222.96 1.00618
bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] 2237 224.343 222.965
bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885] 2238 224.337 222.959
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] 449 246.33 228.463 1.07821
bup protein. [refseq;acc:nm_012071] 2911 0.00001 0.00001 1
bystin. [swissprot;acc:q13895] 384 0 11244.5 10833.3 1.03796
1149 1 233.185 239.505 1.0271
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] 1766 231.732 228.932 1.01223
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] 2473 217.991 218.644 1.003
c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 1554 193.018 196.215 1.01656
c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 1558 192.977 196.171 1.01655
c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 844 170.82 178.033 1.04223
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] 2475 217.571 218.219 1.00298
c18b11 homolog (44.9kd). [refseq;acc:nm_152260] 1625 214.2 217.446 1.01515
c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] 1506 208.339 212.103 1.01807
c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 208 0 10638.4 11846.3 1.11354
321 1 265.959 241.892 1.09949
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 260 196.978 219.421 1.11394
ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] 2577 192.922 192.625 1.00154
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] 1448 222.117 226.532 1.01988

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/