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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1513 to 1562 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
757 nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769] Subtracted 4651.88 5296.78 644.9
signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Divided 5622.89 6260.02 1.11331
758 dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] 3760.3 4185.82 1.11316
nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345] Subtracted 4651.88 5296.78 644.9
759 6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] Divided 4254.62 4736.03 1.11315
phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] Subtracted 6597.56 7240.64 643.08
760 atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] Divided 5870.2 6533.39 1.11298
gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Subtracted 6597.98 7241 643.02
761 beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929]
translation initiation factor if-2. [swissprot;acc:o60841] Divided 5811.51 6467.62 1.1129
762 alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] Subtracted 6597.98 7241 643.02
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Divided 6231.31 6933.9 1.11275
763 6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] 4250.54 4729.67 1.11272
phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] Subtracted 6598.37 7241.32 642.95
764 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] Divided 4250.18 4729.12 1.11269
vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [swissprot;acc:p19065] Subtracted 6654.42 7296.51 642.09
765 polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] Divided 4726.38 5258.95 1.11268
vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [swissprot;acc:p23763] Subtracted 6654.42 7296.51 642.09
766 ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] Divided 6691.93 7445.09 1.11255
vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379] Subtracted 6654.42 7296.51 642.09
767 cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735]
utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Divided 6691.21 7444.22 1.11254
768 adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3] Subtracted 6654.42 7296.51 642.09
ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] Divided 6690.44 7443.29 1.11253
769 vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [swissprot;acc:q16864] 5873.77 6532.44 1.11214
vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] Subtracted 6654.42 7296.51 642.09
770 maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368] 6660.04 7301.81 641.77
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Divided 5874.74 6533.34 1.11211
771 apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595]
signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Subtracted 5622.89 6260.02 637.13
772 probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 3494.31 4129.6 635.29
sec13-related protein. [swissprot;acc:p55735] Divided 5874.76 6533.36 1.11211
773 jm1 protein. [refseq;acc:nm_014008] Subtracted 5794.8 6427.79 632.99
vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4] Divided 5874.74 6533.34 1.11211
774 phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] Subtracted 5384.41 6012.82 628.41
yeast sec31p homolog. [refseq;acc:nm_014933] Divided 5874.76 6533.36 1.11211
775 phenylalanine-trna synthetase. [refseq;acc:nm_006567] Subtracted 5384.41 6012.82 628.41
vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348] Divided 5874.74 6533.33 1.11211
776 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Subtracted 5317.78 5944.25 626.47
ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] Divided 5874.76 6533.36 1.11211
777 dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] 5874.74 6533.34
z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Subtracted 5317.78 5944.25 626.47
778 pp1201 protein. [refseq;acc:nm_022152]
vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313] Divided 5874.63 6533.23 1.11211
779 ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] 5874.76 6533.36
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Subtracted 5317.78 5944.25 626.47
780 sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8] Divided 5874.76 6533.36 1.11211
781 secretory pathway component sec31b-1. [refseq;acc:nm_015490]
sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] Subtracted 5317.78 5944.25 626.47

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/