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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 6958 to 7007 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1740 methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] Rooted 64.9517 67.0286 1.03198
serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] Measured 5878.2 6274.27 1.06738
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Squared 20093.8 18247 1.10121
1741 dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] Rooted 55.2996 53.5864 1.03197
proteasome subunit beta type 9 precursor (ec 3.4.25.1) (proteasome chain 7) (macropain chain 7) (multicatalytic endopeptidase complex chain 7) (ring12 protein) (low molecular mass protein 2). [swissprot;acc:p28065] Squared 29747.7 32753.1 1.10103
serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075] Measured 6297.05 6721.08 1.06734
t-complex 11. [refseq;acc:nm_018679] Ranked 206.595 209.258 1.01289
1742 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Squared 20073.3 18233.1 1.10093
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Measured 6298.76 6722.61 1.06729
myosin viia. [swissprot;acc:q13402] Rooted 61.4677 63.4288 1.0319
tubulin gamma-2 chain (gamma-2 tubulin). [swissprot;acc:q9nrh3] Ranked 206.595 209.258 1.01289
1743 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] Squared 12299.6 13539.1 1.10078
histidine-rich membrane protein ke4. [swissprot;acc:q92504] Measured 6298.81 6722.65 1.06729
pre-mrna cleavage factor i, 59 kda subunit. [refseq;acc:nm_024811] Ranked 218.176 215.402 1.01288
ubiquitin-conjugating enzyme e2 b (ec 6.3.2.19) (ubiquitin-protein ligase b) (ubiquitin carrier protein b) (hr6b) (hhr6b) (e2-17 kda). [swissprot;acc:p23567] Rooted 61.4677 63.4288 1.0319
1744 dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] Squared 13668.7 15045.4 1.10072
microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [swissprot;acc:q15691] Measured 6298.81 6722.65 1.06729
sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901] Ranked 219.423 222.215 1.01272
ubiquitin-conjugating enzyme e2 a (ec 6.3.2.19) (ubiquitin-protein ligase a) (ubiquitin carrier protein a) (hr6a) (hhr6a). [swissprot;acc:p49459] Rooted 61.4677 63.4288 1.0319
1745 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404] Ranked 219.423 222.215 1.01272
cug triplet repeat rna-binding protein 1 (cug-bp1) (rna-binding protein brunol-2) (deadenylation factor cug-bp) (50 kda nuclear polyadenylated rna-binding protein) (eden-bp). [swissprot;acc:q92879] Rooted 62.2833 64.2688 1.03188
epsin 2 isoform b; eps15 binding protein. [refseq;acc:nm_014964] Squared 27935.2 30744.7 1.10057
microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8] Measured 6298.77 6722.62 1.06729
1746 40s ribosomal protein s9. [swissprot;acc:p46781] Squared 14357.1 15800.8 1.10056
cug triplet repeat, rna binding protein 2; elav-type rna-binding protein; cug triplet repeat,rna-binding protein 2; cug triplet repeat, rna-binding protein 2; neuroblastoma apoptosis-related rna-binding protein. [refseq;acc:nm_006561] Rooted 62.2832 64.2687 1.03188
ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181] Ranked 219.423 222.215 1.01272
regucalcin gene promotor region related protein; rgpr-p117. [refseq;acc:nm_033127] Measured 5683.17 6065.55 1.06728
1747 cerebral cell adhesion molecule. [refseq;acc:nm_016174] 9596.59 10241.9 1.06724
n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2] Rooted 60.0062 61.9139 1.03179
potassium channel modulatory factor 1; potassium channel modulatory factor; differentially expressed in branching tubulogenesis 91; zinc finger, zz domain containing 1. [refseq;acc:nm_020122] Squared 25629.5 28203.8 1.10044
tfiih basal transcription factor complex helicase subunit (ec 3.6.1.-) (dna-repair protein complementing xp-d cells) (xeroderma pigmentosum group d complementing protein) (cxpd) (dna excision repair protein ercc-2). [swissprot;acc:p18074] Ranked 188.452 190.845 1.0127
1748 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 215.673 212.971 1.01269
doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602] Measured 6301.03 6724.63 1.06723
serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549] Rooted 65.9275 68.0218 1.03177
solute carrier family 23, member 1 (sodium-dependent vitamin c transporter 1) (hsvct1) (na(+)/l-ascorbic acid transporter 1) (yolk sac permease-like molecule 3). [swissprot;acc:q9uhi7] Squared 25629.5 28203.8 1.10044
1749 dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] Ranked 206.058 203.485 1.01264
electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] Measured 7919.76 8452.01 1.06721
heterogeneous nuclear ribonucleoprotein a3 (hnrnp a3) (d10s102). [swissprot;acc:p51991] Squared 25629.5 28203.8 1.10044
short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547] Rooted 60.4307 58.5724 1.03173
1750 adp-ribosylation factor 4. [swissprot;acc:p18085] Squared 25629.5 28203.8 1.10044
arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144] Measured 5384.89 5746.51 1.06715
dynein light chain 2. [refseq;acc:nm_080677] Rooted 60.4307 58.5724 1.03173
similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2] Ranked 216.27 213.57 1.01264
1751 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] Measured 6011.57 6414.98 1.06711
adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5] Ranked 221.185 223.97 1.01259
coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] Rooted 86.2924 83.6394 1.03172
fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476] Squared 25629.5 28203.8 1.10044
1752 brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] Ranked 216.271 218.991 1.01258
copper-transporting atpase 1 (ec 3.6.3.4) (copper pump 1) (menkes disease-associated protein). [swissprot;acc:q04656] Measured 5941.29 6339.93 1.0671
dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985] Rooted 61.7777 63.7356 1.03169

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/