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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Rank description Network Comparison Type Gene Value Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
1590 prefoldin subunit 1. [swissprot;acc:o60925] Subtracted 6302.76 5875.75 427.01
1591 multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] Divided 6819.38 6364.01 1.07155
secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138] Subtracted 6302.76 5875.75 427.01
1592 26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231] Divided 6271.79 5853.1 1.07153
choline dehydrogenase. [refseq;acc:nm_018397] Subtracted 6302.76 5875.75 427.01
1593 colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508] 6946.75 6520.83 425.92
proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] Divided 5333.78 4977.77 1.07152
1594 glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] Subtracted 6358.78 5933.25 425.53
transportin-sr; importin 12. [refseq;acc:nm_012470] Divided 5555.76 5184.94 1.07152
1595 dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] Subtracted 4185.82 3760.3 425.52
proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [swissprot;acc:p28062] Divided 6805.39 6351.32 1.07149
1596 cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] Subtracted 6084.68 5659.22 425.46
enigma protein; lim domain protein. [refseq;acc:nm_005451] Divided 6070.32 5665.34 1.07148
1597 6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] Subtracted 6463.9 6038.46 425.44
eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371] Divided 6070.32 5665.34 1.07148
1598 lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] 5430.41 5068.17 1.07147
mitochondrial ribosomal protein l30 isoform a. [refseq;acc:nm_145212] Subtracted 6349.04 5923.66 425.38
1599 26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524]
40s ribosomal protein s24 (s19). [swissprot;acc:p16632] Divided 5554.97 5184.45 1.07147
1600 14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758] 6788.96 6336.22 1.07145
wd-repeat protein bing4. [swissprot;acc:o15213] Subtracted 4491.65 4066.56 425.09
1601 cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] 6085.22 5660.17 425.05
spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [swissprot;acc:o15020] Divided 5605.8 5232.14 1.07142
1602 26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242] Subtracted 6244.37 5819.39 424.98
spectrin beta chain, brain 1 (spectrin, non-erythroid beta chain 1) (beta-ii spectrin) (fodrin beta chain). [swissprot;acc:q01082] Divided 5605.8 5232.14 1.07142
1603 phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394]
porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397] Subtracted 5337.95 4913.07 424.88
1604 malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822] Divided 6617.91 6176.82 1.07141
phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [swissprot;acc:q9nry7] Subtracted 6685.05 6260.43 424.62
1605 itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [refseq;acc:nm_031483] Divided 6617.91 6176.82 1.07141
phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] Subtracted 6684.31 6259.8 424.51
1606 5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] Divided 5606.53 5232.99 1.07138
phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [swissprot;acc:q9nrq2] Subtracted 6684.3 6259.8 424.5
1607 putative ribosomal rna methyltransferase 1 (ec 2.1.1.-) (rrna (uridine-2'-o-)-methyltransferase) (jm23 protein). [swissprot;acc:q9uet6] Divided 5606.53 5232.99 1.07138
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Subtracted 4803.59 4379.28 424.31
1608 transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] 7444.06 7019.78 424.28
ubiquitin. [swissprot;acc:p02248] Divided 6597.55 6158.22 1.07134
1609 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] 6242.44 5826.74
serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075] Subtracted 6721.08 6297.05 424.03
1610 eif-5a2 protein. [refseq;acc:nm_020390] Divided 6665.83 6222.4 1.07126
proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] Subtracted 6503.12 6079.19 423.93
1611 cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] Divided 5132.35 5497.73 1.07119
molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007] Subtracted 6503.12 6079.19 423.93
1612 anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885]
eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159] Divided 6655.12 6212.98 1.07116
1613 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] Subtracted 6503.12 6079.19 423.93
mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] Divided 6464.5 6035.6 1.07106
1614 nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946]
proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] Subtracted 6503.12 6079.19 423.93
1615 lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12] Divided 6464.5 6035.6 1.07106

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/