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

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/