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 Filtered Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 2080 to 2129 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
260 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Measured 0 1949.36 2202 1.1296
261 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Ranked 12448.9 11393.9 1.09259
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Rooted 22.315 24.6198 1.10328
apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] Squared 135280 170628 1.2613
c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Measured 1295.81 1463.55 1.12945
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Ranked 1 219.421 196.978 1.11394
pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] Squared 48127.9 62245.6 1.29334
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Rooted 62.3337 70.0738 1.12417
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Measured 4247.36 5192.61 1.22255
262 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Squared 0 2463.89 3102.4 1.25915
60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Rooted 26.0693 28.761 1.10325
adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] Measured 764.479 676.971 1.12926
cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] 1 24896.4 20431.7 1.21852
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Ranked 219.421 196.978 1.11394
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Squared 26157.6 20236.2 1.29261
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Rooted 59.4073 66.7002 1.12276
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] Ranked 0 3464 3778 1.09065
263 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Squared 1 26157.6 20236.2 1.29261
adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] Rooted 0 4.79583 4.3589 1.10024
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Ranked 13573.3 14801.2 1.09046
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] 1 219.421 196.978 1.11394
paxillin. [swissprot;acc:p49023] Rooted 59.4073 66.7002 1.12276
ribosomal protein l10-like protein. [refseq;acc:nm_080746] Squared 0 2463.98 3102.52 1.25915
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] Measured 1843 1633 1.1286
trs85 homolog. [swissprot;acc:q9y2l5] 1 24896.4 20431.7 1.21852
264 60s ribosomal protein l12. [swissprot;acc:p30050] Squared 0 3686.65 4639.46 1.25845
adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] 1 26157.6 20236.2 1.29261
arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681] Ranked 0 10037.1 10935.1 1.08947
cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Measured 1 4987.58 4094.57 1.2181
mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Ranked 219.421 196.978 1.11394
sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] Measured 0 3336.48 2957.12 1.12829
transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] Rooted 11.0015 9.99917 1.10024
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 1 66.1122 74.1438 1.12148
265 40s ribosomal protein s29. [swissprot;acc:p30054] 0 26.1023 28.6733 1.0985
60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Squared 3687.69 4640.77 1.25845
60s ribosomal protein l9. [swissprot;acc:p32969] Measured 1685.44 1894.01 1.12375
glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] Ranked 13653.8 14874 1.08937
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Squared 1 26157.6 20236.2 1.29261
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Ranked 225.217 202.459 1.11241
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Rooted 56.031 62.8281 1.12131
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Measured 24806.9 20369.9 1.21782
266 aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] 0 1475.05 1312.91 1.1235
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 1 24806.9 20369.9 1.21782
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Squared 0 3687.33 4640.32 1.25845
fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] 1 26157.6 20236.2 1.29261
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Rooted 66.1064 74.1074 1.12103
transcription factor btf3 homolog 3. [swissprot;acc:q13892] Ranked 0 13483.3 14685.4 1.08915
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Rooted 39.5626 36.099 1.09595
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Ranked 1 241.07 267.88 1.11121
267 density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]

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/