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 1510 to 1559 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
755 voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303] Low confidence 8233.47 8581.15 1.04223
756 topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] High confidence 4725.28 5261.06 1.11339
voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [swissprot;acc:q14722] Low confidence 8232.8 8580.24 1.0422
757 signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] High confidence 5622.89 6260.02 1.11331
surfeit locus protein 1. [swissprot;acc:q15526] Low confidence 7988.86 8325.55 1.04214
758 dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] High confidence 3760.3 4185.82 1.11316
growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] Low confidence 7862.29 8193.26 1.0421
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] High confidence 4254.62 4736.03 1.11315
cytochrome p450 3a43 (ec 1.14.14.1). [swissprot;acc:q9hb55] Low confidence 8087.27 8427.25 1.04204
760 atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] High confidence 5870.2 6533.39 1.11298
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Low confidence 7152.13 7452.64 1.04202
761 electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] 8831.38 9202.43 1.04201
translation initiation factor if-2. [swissprot;acc:o60841] High confidence 5811.51 6467.62 1.1129
762 pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] 6231.31 6933.9 1.11275
suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] Low confidence 8056.9 8395.02 1.04197
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] High confidence 4250.54 4729.67 1.11272
cytochrome p450 3a5 (ec 1.14.14.1) (cypiiia5) (p450-pcn3). [swissprot;acc:p20815] Low confidence 8087.04 8426.3 1.04195
764 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] High confidence 4250.18 4729.12 1.11269
cytochrome p450 3a7 (ec 1.14.14.1) (cypiiia7) (p450-hfla). [swissprot;acc:p24462] Low confidence 8084.46 8423.24 1.04191
765 copper-transporting atpase 1 (ec 3.6.3.4) (copper pump 1) (menkes disease-associated protein). [swissprot;acc:q04656] 8631.91 8993.16 1.04185
polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] High confidence 4726.38 5258.95 1.11268
766 cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] Low confidence 7591.4 7909.08 1.04185
ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] High confidence 6691.93 7445.09 1.11255
767 intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] Low confidence 10504.2 10082.3 1.04185
utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] High confidence 6691.21 7444.22 1.11254
768 synaptic vesicle protein 2b homolog. [refseq;acc:nm_014848] Low confidence 8135.44 8475.48 1.0418
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] High confidence 6690.44 7443.29 1.11253
769 splicing factor, arginine/serine-rich 7 (splicing factor 9g8). [swissprot;acc:q16629] Low confidence 7730.27 8053.27 1.04178
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] High confidence 5873.77 6532.44 1.11214
770 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Low confidence 7730.27 8053.27 1.04178
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] High confidence 5874.74 6533.34 1.11211
771 apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595]
cytochrome p450 3a4 (ec 1.14.13.67) (quinine 3-monooxygenase) (cypiiia4) (nifedipine oxidase) (nf-25) (p450-pcn1). [swissprot;acc:p08684] Low confidence 8081.2 8418.72 1.04177
772 sec13-related protein. [swissprot;acc:p55735] High confidence 5874.76 6533.36 1.11211
zinc finger protein 183. [swissprot;acc:o15541] Low confidence 7534.02 7848.32 1.04172
773 tensin. [refseq;acc:nm_022648] 7319.93 7625.29
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] High confidence 5874.74 6533.34 1.11211
774 coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488] Low confidence 6886.05 7173.24 1.04171
yeast sec31p homolog. [refseq;acc:nm_014933] High confidence 5874.76 6533.36 1.11211
775 protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735] Low confidence 6886.05 7173.24 1.04171
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] High confidence 5874.74 6533.33 1.11211
776 ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] 5874.76 6533.36
ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Low confidence 8380.36 8729.64 1.04168
777 dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] High confidence 5874.74 6533.34 1.11211
synaptic vesicle glycoprotein 2. [refseq;acc:nm_014849] Low confidence 8135.08 8474.03 1.04167
778 ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] 8379.93 8729.12
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] High confidence 5874.63 6533.23 1.11211
779 ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] 5874.76 6533.36
ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] Low confidence 8379.96 8729.16 1.04167
780 calcineurin b subunit isoform 1 (protein phosphatase 2b regulatory subunit 1) (protein phosphatase 3 regulatory subunit b alpha isoform 1). [swissprot;acc:p06705] 7325.81 7631.04

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/