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 Value Type Rank description Interaction Map network_comparison Network Comparison Type Filtered red green
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 19268 in total
Value Type  : Measured
Rank
description
Interaction Map
network_comparison
Network Comparison Type
Filtered
red
green
398 histone h2b.c (h2b/c). [swissprot;acc:q99880] High confidence 1.04078 Divided 0 2132.04 2218.98
interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Low confidence 1.10405 135.294 149.371
mus81 endonuclease. [refseq;acc:nm_025128] 431.89 Subtracted 1 8847.94 9279.83
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] High confidence 29.036 0 112.666 141.702
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] 1.16125 Divided 1 5084.26 5904.1
399 dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] Low confidence 1.05272 7680.62 8085.57
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 118.779 Subtracted 0 863.737 744.958
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] High confidence 1.03981 Divided 548.5 527.5
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 1.16109 1 5201.41 4479.76
sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503] 29 Subtracted 0 107 78
similar to hepatocellular carcinoma-associated antigen hca557b. [refseq;acc:nm_145280] Low confidence 431.89 1 8847.94 9279.83
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] 1.10398 Divided 0 250.379 226.797
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] High confidence 938.93 Subtracted 1 4633.92 5572.85
400 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] 1.16109 Divided 5201.41 4479.76
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 938.837 Subtracted 1834.73 895.893
hepatocellularcarcinoma-associated antigen hca557a. [refseq;acc:nm_015433] Low confidence 431.89 8847.94 9279.83
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] 118.76 0 1940.37 2059.13
mad protein (max dimerizer). [swissprot;acc:q05195] 1.05272 Divided 1 6970.25 7337.73
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] High confidence 1.03981 0 548.5 527.5
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 27.6038 Subtracted 65.2968 37.693
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Low confidence 1.10389 Divided 1326.18 1201.37
401 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] High confidence 1.16109 1 5201.41 4479.76
dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Low confidence 430.76 Subtracted 7559.1 7989.86
gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] 1.0527 Divided 10800.7 10260
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] High confidence 938.328 Subtracted 1835.3 896.972
jm5 protein. [refseq;acc:nm_007075] Low confidence 118.157 0 981.333 1099.49
mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] High confidence 27.2 1549.26 1522.06
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] 1.03981 Divided 548.5 527.5
transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525] Low confidence 1.10385 1277.86 1410.56
402 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] 429.17 Subtracted 1 8730.02 9159.19
arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] High confidence 937.26 6230.94 7168.2
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] 1.16109 Divided 5201.41 4479.76
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] 27.1855 Subtracted 0 12.6208 39.8063
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 1.03981 Divided 548.5 527.5
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Low confidence 1.10305 1643.27 1812.61
sedlin. [swissprot;acc:o14582] 117.98 Subtracted 181.896 299.876
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] 1.05269 Divided 1 7934.21 8352.26
403 fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] High confidence 1.16109 5201.41 4479.76
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Low confidence 117.804 Subtracted 0 864.333 746.529
hepatocellularcarcinoma-associated antigen hca557a. [refseq;acc:nm_015433] 1.1028 Divided 2800 2539
maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] High confidence 25.72 Subtracted 2290.09 2264.37
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] 1.03981 Divided 548.5 527.5
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Low confidence 428.22 Subtracted 1 7398.26 7826.48
ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] High confidence 931.61 6259.3 7190.91
seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] Low confidence 1.05269 Divided 8853.13 9319.56
404 adiponectin receptor 2. [refseq;acc:nm_024551] 428.16 Subtracted 7170.39 7598.55
dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] 117.75 0 1709.74 1591.99
importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] High confidence 929.51 1 7802.31 8731.82
kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [swissprot;acc:q02241] Low confidence 1.05265 Divided 10008.8 9508.16
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] High confidence 1.16109 5201.41 4479.76

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/