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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Gene description Value Type Rank Filtered Network Comparison Type network_comparison Interaction Map green red
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
network_comparison
green
red
blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] 419 0 1.02991 17183 16684
1928 1 1.01001 198.935 196.964
bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 114 0 1.19525 10603.2 8871.11
1748 1 1.01269 212.971 215.673
bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] 793 1.04578 234.511 224.244
bone morphogenetic protein 5 precursor (bmp-5). [swissprot;acc:p22003] 3069 1 0.00001 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] 91 0 1.24387 11127.5 13841.2
2773 1 1 0.00001 0.00001
brachyury protein (t protein). [swissprot;acc:o15178] 2040 1.00854 208.803 210.586
brain protein 16. [refseq;acc:nm_016458] 49 0 1.41927 4854.99 6890.54
1847 1 1.011 219.195 216.811
brain protein 44. [swissprot;acc:o95563] 742 1.05111 120.078 126.215
branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] 2672 1.00102 210.741 210.957
branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] 2687 1.00087 210.755 210.939
brca1 associated protein. [refseq;acc:nm_006768] 502 0 1 0.00001 0.00001
3161 1
brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] 1752 1.01258 218.991 216.271
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 1.10356 265.717 240.782
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 229 1.12028 202.094 226.401
breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] 939 1.03588 224.27 216.501
breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 691 1.05532 206.195 217.602
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 1.00057 220.395 220.521
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 1.03586 205.085 212.44
bromodomain and phd finger-containing protein 3 (fragment). [swissprot;acc:q9uld4] 3149 1 0.00001 0.00001
bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [refseq;acc:nm_013263] 2747 1.00018 201.514 201.477
bromodomain-containing protein 1 (br140-like protein). [swissprot;acc:o95696] 3139 1 0.00001 0.00001
bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] 2241 1.00618 224.338 222.96
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 1 0.00001 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] 449 1.07821 246.33 228.463
bup protein. [refseq;acc:nm_012071] 2911 1 0.00001 0.00001
bystin. [swissprot;acc:q13895] 384 0 1.03796 11244.5 10833.3
1149 1 1.0271 233.185 239.505
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 1.01223 231.732 228.932
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 1.003 217.991 218.644
c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 1554 1.01656 193.018 196.215
c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 1558 1.01655 192.977 196.171
c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 844 1.04223 170.82 178.033
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 1.00298 217.571 218.219
c18b11 homolog (44.9kd). [refseq;acc:nm_152260] 1625 1.01515 214.2 217.446
c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] 1506 1.01807 208.339 212.103
c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 208 0 1.11354 10638.4 11846.3
321 1 1.09949 265.959 241.892
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 260 1.11394 196.978 219.421
ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] 2577 1.00154 192.922 192.625
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 1.01988 222.117 226.532

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/