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.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4836 to 4885 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1209 succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [swissprot;acc:p21912] Ranked 207.931 213.175 1.02522
1210 homeobox protein dlx-3. [swissprot;acc:o60479] Squared 19317.7 21958.6 1.13671
kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139] Ranked 224.764 219.241 1.02519
proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80] Rooted 61.3876 64.2125 1.04602
trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6] Measured 6410.73 6962.22 1.08603
1211 activated p21cdc42hs kinase. [refseq;acc:nm_005781] Squared 19317.7 21958.6 1.13671
chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265] Ranked 214.364 219.759 1.02517
dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] Rooted 67.2521 70.3462 1.04601
gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616] Measured 6410.73 6962.22 1.08603
1212 hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] 4077.89 4428.28 1.08592
homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8] Rooted 61.3832 64.2055 1.04598
kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9] Ranked 214.364 219.759 1.02517
mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093] Squared 19317.7 21958.6 1.13671
1213 40s ribosomal protein s8. [swissprot;acc:p09058] Rooted 61.4774 64.3044 1.04598
branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] Measured 5890.62 6396.53 1.08588
conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746] Ranked 214.364 219.759 1.02517
ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Squared 20823.1 23668.4 1.13664
1214 dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Rooted 67.2519 70.3434 1.04597
ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Squared 20823.1 23668.4 1.13664
kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] Ranked 214.364 219.759 1.02517
mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318] Measured 6001.16 6515.9 1.08577
1215 branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] 5892.05 6397.28 1.08575
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Ranked 218.268 212.916 1.02514
mitotic checkpoint protein bub3. [swissprot;acc:o43684] Rooted 60.2183 62.9735 1.04575
nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Squared 20823.1 23668.4 1.13664
1216 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] 20823.5 23668.7 1.13663
fibulin-2 precursor. [swissprot;acc:p98095] Measured 8670.59 9412.9 1.08561
retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] Ranked 218.269 212.918 1.02513
zinc finger protein 207. [swissprot;acc:o43670] Rooted 60.2183 62.9735 1.04575
1217 cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708] Measured 6021.21 6536.45 1.08557
cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] Rooted 61.4717 64.2826 1.04573
gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [refseq;acc:nm_013334] Squared 22101.6 25118.6 1.13651
glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] Ranked 211.959 217.258 1.025
1218 cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184] Measured 5736 6226.52 1.08552
fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519] Ranked 211.959 217.258 1.025
gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] Squared 22101.6 25118.6 1.13651
hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] Rooted 51.9837 54.3601 1.04571
1219 coactosin-like protein. [swissprot;acc:q14019] Ranked 211.959 217.258 1.025
cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] Rooted 61.4767 64.2857 1.04569
myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Squared 20836.6 23679.5 1.13644
tcd37 homolog; prune. [refseq;acc:nm_021222] Measured 5735.95 6226.46 1.08552
1220 40s ribosomal protein s3a. [swissprot;acc:p49241] Squared 19516.8 22178 1.13635
cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623] Measured 5735.65 6226.13 1.08551
dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0] Rooted 58.0178 60.6658 1.04564
uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] Ranked 211.959 217.258 1.025
1221 casein kinase i alpha s-like. [refseq;acc:nm_145203] Squared 20055.2 22788 1.13626
cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649] Measured 5736.34 6226.88 1.08551
glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] Rooted 66.3775 69.4004 1.04554
probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] Ranked 211.959 217.258 1.025
1222 casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] Squared 20055.2 22788 1.13626

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/