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 Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2408 to 2457 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1204 suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524] Divided 5946.33 6459.79 1.08635
1205 glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234]
phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] Subtracted 5462.88 5958.12 495.24
1206 asc-1 complex subunit p100. [refseq;acc:nm_032204] Divided 5946.33 6459.79 1.08635
synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] Subtracted 5460.49 5954.62 494.13
1207 fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [swissprot;acc:p20071] Divided 5946.33 6459.79 1.08635
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Subtracted 6105.93 6599.41 493.48
1208 meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565] Divided 5913.73 6423.98 1.08628
orphan nuclear receptor tr2. [swissprot;acc:p13056] Subtracted 6105.69 6599.06 493.37
1209 bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814] Divided 5420.87 5887.53 1.08609
dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0] Subtracted 5147.9 5641.25 493.35
1210 mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [swissprot;acc:q15750] 6051.23 6544.17 492.94
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] Divided 6410.73 6962.22 1.08603
1211 gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616]
similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245] Subtracted 5807.83 6300.47 492.64
1212 ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665]
hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] Divided 4077.89 4428.28 1.08592
1213 branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] 5890.62 6396.53 1.08588
g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] Subtracted 6140.18 6632.24 492.06
1214 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] Divided 6001.16 6515.9 1.08577
nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] Subtracted 3879.99 4371.24 491.25
1215 branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] Divided 5892.05 6397.28 1.08575
cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649] Subtracted 5736.34 6226.88 490.54
1216 cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184] 5736 6226.52 490.52
fibulin-2 precursor. [swissprot;acc:p98095] Divided 8670.59 9412.9 1.08561
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] 6021.21 6536.45 1.08557
tcd37 homolog; prune. [refseq;acc:nm_021222] Subtracted 5735.95 6226.46 490.51
1218 cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348] 5735.74 6226.23 490.49
cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184] Divided 5736 6226.52 1.08552
1219 cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623] Subtracted 5735.65 6226.13 490.48
tcd37 homolog; prune. [refseq;acc:nm_021222] Divided 5735.95 6226.46 1.08552
1220 cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623] 5735.65 6226.13 1.08551
mesoderm induction early response 1. [refseq;acc:nm_020948] Subtracted 6291.89 6781.6 489.71
1221 cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649] Divided 5736.34 6226.88 1.08551
proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [swissprot;acc:p25788] Subtracted 6291.89 6781.6 489.71
1222 cyclin c. [swissprot;acc:p24863] 6200.93 6690.57 489.64
cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348] Divided 5735.74 6226.23 1.08551
1223 serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [swissprot;acc:q9upe1] Subtracted 5894.47 6383.73 489.26
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Divided 6011.44 6524.55 1.08536
1224 gtp binding protein 2. [refseq;acc:nm_019096] Subtracted 5894.47 6383.73 489.26
splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427] Divided 4331.35 4700.91 1.08532
1225 apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] 5546.5 6019.57 1.08529
cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941] Subtracted 5894.47 6383.73 489.26
1226 dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135]
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Divided 5997.24 6508.62 1.08527
1227 nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838] Subtracted 5144.74 5634 489.26
pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] Divided 5973.95 6483.32 1.08527
1228 dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] 5998.58 6509.65 1.0852
sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691] Subtracted 5894.47 6383.73 489.26
1229 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] Divided 5998.69 6509.74 1.08519

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/