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 1601 to 1650 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
201 60s ribosomal protein l11. [swissprot;acc:p39026] Ranked Subtracted 241.828 267.346 25.518
calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Squared Divided 71033.4 95440.2 1.3436
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] Rooted Subtracted 138.375 127.926 10.449
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] Divided 61.2893 70.3856 1.14842
mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] Squared Subtracted 42411.6 55802.1 13390.5
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Ranked Divided 240.133 211.382 1.13601
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Measured 4810.22 6075.04 1.26294
translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Subtracted 10603.5 12069.5 1466
202 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Ranked 240.758 266.079 25.321
calsyntenin-1 precursor. [swissprot;acc:o94985] Measured 10603.5 12069.5 1466
calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Squared Divided 71030.1 95434.8 1.34358
enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Measured 4812.01 6076.09 1.26269
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Squared Subtracted 42411.6 55802.1 13390.5
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Ranked Divided 201.478 228.784 1.13553
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Rooted 57.3527 65.7973 1.14724
trs85 homolog. [swissprot;acc:q9y2l5] Subtracted 138.375 127.926 10.449
203 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Ranked 240.758 266.078 25.32
autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] Measured Divided 11757.8 9352.11 1.25723
ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Ranked 201.515 228.752 1.13516
hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Squared 20988.2 15632.1 1.34263
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Subtracted 42411.6 55802.1 13390.5
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Measured 10603.5 12069.5 1466
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Rooted Divided 46.3291 53.1063 1.14628
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Subtracted 138.032 127.651 10.381
204 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Ranked 268.632 243.588 25.044
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Rooted 138.032 127.651 10.381
protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Measured 10603.5 12069.4 1465.9
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Ranked Divided 201.515 228.752 1.13516
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Measured 4512.19 5655.52 1.25339
Rooted 55.8956 63.9636 1.14434
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Squared 12326.4 16522.9 1.34045
sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] Subtracted 42411.6 55802.1 13390.5
205 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Ranked 268.635 243.592 25.043
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Divided 228.1 200.968 1.13501
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Squared 12326.4 16522.9 1.34045
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Rooted Subtracted 114.309 124.527 10.218
small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Measured Divided 4512.19 5655.52 1.25339
Rooted 55.8956 63.9636 1.14434
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Squared Subtracted 40982.6 54272.3 13289.7
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Measured 10603.5 12069.4 1465.9
206 40s ribosomal protein s15a. [swissprot;acc:p39027] Ranked 241.411 266.414 25.003
atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Measured Divided 5720.25 4577.5 1.24965
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] Squared 12326.4 16522.9 1.34045
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Rooted 140.508 122.878 1.14348
gk001 protein. [refseq;acc:nm_020198] Measured Subtracted 10603.5 12069.4 1465.9
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Ranked Divided 228.085 201.006 1.13472
mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Squared Subtracted 46739.9 59134.5 12394.6
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Rooted 45.4558 55.5995 10.1437
207 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Divided 140.508 122.878 1.14348
calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Measured Subtracted 10600.3 12065.2 1464.9

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/