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 2091 to 2140 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
523 neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837] Squared 53174 44377.4 1.19822
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Rooted 66.377 72.2842 1.08899
524 aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154] Squared 53174 44377.4 1.19822
aquaporin 5. [swissprot;acc:p55064] Measured 10640 12117.6 1.13887
brain protein 44. [swissprot;acc:o95563] Rooted 113.374 123.463 1.08899
exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] Ranked 215.237 230.07 1.06891
525 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Squared 53174 44377.4 1.19822
exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4] Ranked 215.237 230.07 1.06891
lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Measured 10639.8 12117.3 1.13887
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Rooted 113.374 123.463 1.08899
526 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Measured 10639.9 12117.4 1.13886
electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117] Squared 31189.6 37352.8 1.1976
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Ranked 250.538 234.401 1.06884
septin 6. [swissprot;acc:q14141] Rooted 113.169 123.23 1.0889
527 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Ranked 248.56 232.579 1.06871
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Rooted 153.191 166.771 1.08865
protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Measured 4775.11 5438.18 1.13886
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Squared 18011.9 21552.8 1.19659
528 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Measured 10635.3 12111.4 1.13879
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] Squared 10606 8868.81 1.19588
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Rooted 66.941 72.7546 1.08685
yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Ranked 222.146 237.393 1.06864
529 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] 251.653 235.506 1.06856
mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Measured 8600.02 9792.49 1.13866
nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] Rooted 50.3239 54.6658 1.08628
sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] Squared 28990.9 34656.4 1.19542
530 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] Rooted 50.6537 46.6413 1.08603
monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283] Squared 27179.5 32490.8 1.19542
peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Measured 8600.02 9792.49 1.13866
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Ranked 227.483 212.994 1.06803
531 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] Rooted 50.6537 46.6413 1.08603
nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Ranked 223.356 209.149 1.06793
solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] Squared 28980.7 34643.6 1.1954
transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] Measured 4651.88 5296.78 1.13863
532 kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Squared 28967 34626.4 1.19537
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Rooted 107.961 117.197 1.08555
thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] Measured 4651.88 5296.78 1.13863
zinc finger-like protein 9. [refseq;acc:nm_033414] Ranked 250.942 235.004 1.06782
533 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Rooted 50.8036 46.8198 1.08509
membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] Ranked 250.942 235.004 1.06782
nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769] Measured 4651.88 5296.78 1.13863
sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] Squared 28937.1 34588.8 1.19531
534 40s ribosomal protein s16. [swissprot;acc:p17008] Rooted 50.8036 46.8198 1.08509
dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887] Squared 27034.1 32301.8 1.19485
guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] Ranked 250.942 235.004 1.06782
nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345] Measured 4651.88 5296.78 1.13863
535 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Rooted 50.8041 46.8218 1.08505
dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434] Ranked 236.662 252.708 1.0678
maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368] Squared 37147.5 44372.1 1.19448
translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Measured 10603.5 12069.5 1.13826

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/