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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Gene Rank Value Type description Network Comparison Type Interaction Map red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 925 to 974 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
Network Comparison Type
red
network_comparison
green
116 Squared myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Divided 19321 1.54043 12542.6
p66 alpha. [refseq;acc:nm_017660] Subtracted 81888.8 25582.3 56306.5
Rooted amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Divided 80.4705 1.26165 101.526
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Subtracted 40.6302 15.185 25.4452
117 Measured metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 9276.47 2186.1 7090.37
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Divided 21185 1.34491 28492
Ranked high-mobility group 20a. [refseq;acc:nm_018200] Subtracted 208.588 36.81 171.778
neuralized-like. [refseq;acc:nm_004210] Divided 332.326 1.24491 266.948
Squared cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] 211446 1.53866 137422
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Subtracted 81888.8 25582.3 56306.5
Rooted guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] 40.5691 15.1428 25.4263
transcription factor jun-b. [swissprot;acc:p17275] Divided 63.4173 1.25409 79.5311
118 Measured beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Subtracted 9275.1 2185.45 7089.65
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Divided 21185 1.34491 28492
Ranked nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] 284.753 1.24382 228.934
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Subtracted 274.027 36.237 237.79
Squared poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Divided 210445 1.53858 136779
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Subtracted 81888.8 25582.3 56306.5
Rooted homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Divided 50.3065 1.2519 62.9788
nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Subtracted 37.2205 14.9859 52.2064
119 Measured acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 12998.5 2139.7 15138.2
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Divided 21185 1.34491 28492
Ranked adiponectin receptor 2. [refseq;acc:nm_024551] Subtracted 281.582 35.211 246.371
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Divided 318.982 1.23157 259.004
Squared cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Subtracted 81606.8 25391 56215.8
exocyst complex component sec5. [swissprot;acc:q96kp1] Divided 210335 1.53848 136716
Rooted serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] Subtracted 63.6507 14.938 48.7127
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Divided 50.3247 1.25166 62.9892
120 Measured high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] 5136.78 1.34247 6895.98
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Subtracted 4932.27 2101.02 7033.29
Ranked nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 227.199 34.484 192.715
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Divided 269.278 1.21699 327.709
Squared g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Subtracted 81592.1 25381 56211.1
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Divided 210199 1.53836 136638
Rooted guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Subtracted 40.081 14.9264 25.1546
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Divided 50.3333 1.25154 62.9942
121 Measured jun dimerization protein. [refseq;acc:nm_130469] Subtracted 4932.27 2101.02 7033.29
transcription factor jun-b. [swissprot;acc:p17275] Divided 5579.18 1.3422 7488.4
Ranked cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 269.254 1.2169 327.655
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Subtracted 227.202 34.379 192.823
Squared cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] 81527.6 25337 56190.6
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Divided 199594 1.53509 130021
Rooted homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 50.339 1.25147 62.9975
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] Subtracted 63.6205 14.7367 48.8838
122 Measured fos-related antigen 2. [swissprot;acc:p15408] 4941.95 2095.16 7037.11
high-mobility group 20a. [refseq;acc:nm_018200] Divided 5140.14 1.34112 6893.53
Ranked cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Subtracted 199.949 34.238 234.187
potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Divided 269.248 1.21688 327.642
Squared cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 201896 1.53061 131906
g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Subtracted 81520.8 25332.3 56188.5

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/