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 2425 to 2474 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1213 branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] Divided 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
transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [swissprot;acc:p35269] Subtracted 5144.74 5634 489.26
1230 cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [swissprot;acc:p18850] 5894.47 6383.73
dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] Divided 5678.02 6161.65 1.08518
1231 probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2] 5132.68 5569.54 1.08511
sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137] Subtracted 5894.47 6383.73 489.26
1232 nuclear factor, interleukin 3 regulated. [refseq;acc:nm_005384] Divided 5869.24 6367.8 1.08494
xap-5 protein (hxc-26 protein). [swissprot;acc:q14320] Subtracted 5894.47 6383.73 489.26
1233 midasin (midas-containing protein). [swissprot;acc:q9nu22] 4483.08 4971.62 488.54
tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] Divided 6004.54 6514.24 1.08489
1234 programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] Subtracted 4749.52 5237.77 488.25
similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245] Divided 5807.83 6300.47 1.08482
1235 ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665]
p47 protein isoform a. [refseq;acc:nm_016143] Subtracted 6444.4 6932.39 487.99
1236 p10-binding protein. [refseq;acc:nm_024491] Divided 5594.18 6067.49 1.08461
presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] Subtracted 6153.36 6640.77 487.41
1237 gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936]
tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8] Divided 5873.56 6370.31 1.08457

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/