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 network_comparison green
Results: HTML CSV LaTeX Showing element 2451 to 2500 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
network_comparison
green
1226 dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135] Subtracted 5894.47 489.26 6383.73
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Divided 5997.24 1.08527 6508.62
1227 nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838] Subtracted 5144.74 489.26 5634
pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] Divided 5973.95 1.08527 6483.32
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 1.0852 6509.65
sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691] Subtracted 5894.47 489.26 6383.73
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 1.08519 6509.74
transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [swissprot;acc:p35269] Subtracted 5144.74 489.26 5634
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 1.08518 6161.65
1231 probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2] 5132.68 1.08511 5569.54
sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137] Subtracted 5894.47 489.26 6383.73
1232 nuclear factor, interleukin 3 regulated. [refseq;acc:nm_005384] Divided 5869.24 1.08494 6367.8
xap-5 protein (hxc-26 protein). [swissprot;acc:q14320] Subtracted 5894.47 489.26 6383.73
1233 midasin (midas-containing protein). [swissprot;acc:q9nu22] 4483.08 488.54 4971.62
tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] Divided 6004.54 1.08489 6514.24
1234 programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] Subtracted 4749.52 488.25 5237.77
similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245] Divided 5807.83 1.08482 6300.47
1235 ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665]
p47 protein isoform a. [refseq;acc:nm_016143] Subtracted 6444.4 487.99 6932.39
1236 p10-binding protein. [refseq;acc:nm_024491] Divided 5594.18 1.08461 6067.49
presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] Subtracted 6153.36 487.41 6640.77
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 1.08457 6370.31
1238 potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196] Subtracted 6153.36 487.41 6640.77
sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676] Divided 5873.56 1.08457 6370.31
1239 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 5654.53 6132.76
kccr13l. [refseq;acc:nm_139179] Subtracted 5538.8 486.71 6025.51
1240 dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609]
retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] Divided 5654.54 1.08456 6132.69
1241 26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [swissprot;acc:q13200] 6436.19 1.08451 6980.13
serologically defined colon cancer antigen 16. [refseq;acc:nm_006649] Subtracted 6268.94 486.63 6755.57
1242 delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] 6274.62 486.16 6760.78
ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Divided 11143.5 1.08439 10276.3
1243 phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] Subtracted 5885 486.14 6371.14
ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] Divided 11143.5 1.08439 10276.3
1244 3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405] Subtracted 5885 486.14 6371.14
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Divided 4835.55 1.08431 5243.23
1245 3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213] Subtracted 5885 486.14 6371.14
casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862] Divided 4835.55 1.08431 5243.23
1246 methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5] Subtracted 5110.6 486.13 5596.73
p53-related protein kinase (ec 2.7.1.-) (nori-2). [swissprot;acc:q96s44] Divided 5346.11 1.08429 5796.72
1247 kinesin protein. [refseq;acc:nm_032559] Subtracted 5356.23 485.92 5842.15
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] Divided 6278.76 1.08421 6807.51
1248 ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] Subtracted 5358.18 485.55 5843.73
protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [swissprot;acc:p17706] Divided 6275.86 1.08415 6803.95
1249 kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139] Subtracted 5359.72 485.25 5844.97
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Divided 4413.55 1.08407 4784.6
1250 caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844] Subtracted 4970.21 485.13 5455.34
huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] Divided 10733.4 1.0839 9902.6

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/