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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Filtered Value Type network_comparison green Gene Interaction Map Network Comparison Type red Rank description
Results: HTML CSV LaTeX Showing element 451 to 500 of 77072 in total
Filtered  : 0
Value Type  : Measured
Network Comparison Type  : Divided
network_comparison
green
Interaction Map
red
Rank
description
1.05438 3969.94 Low confidence 4185.81 541 collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]
4658.69 High confidence 4912.01 376 protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031]
1.0545 2227.75 Low confidence 2112.62 540 protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237]
1.05454 1926.2 1826.57 539 importin 7; ran-binding protein 7. [refseq;acc:nm_006391]
1.05457 1224.9 1161.52 538 aldehyde dehydrogenase, dimeric nadp-preferring (ec 1.2.1.5) (aldh class 3) (aldhiii). [swissprot;acc:p30838]
1.05472 1245.48 1180.86 537 inositol polyphosphate-5-phosphatase, 145kda; hp51cn; inositol polyphosphate-5-phosphatase, 145kd. [refseq;acc:nm_005541]
1.05484 959.463 1012.08 536 keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]
1.05494 1284.05 1354.59 535 cytochrome c oxidase polypeptide viia-heart, mitochondrial precursor (ec 1.9.3.1) (cytochrome c oxidase subunit viia-h) (cox viia-m). [swissprot;acc:p24310]
1.05495 740.494 781.187 534 adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377]
1.05516 2312.27 2439.81 533 myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]
1.05527 2452.23 High confidence 2323.8 374 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741]
375 estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061]
1.05537 958.745 Low confidence 1011.83 531 keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]
532 keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]
958.753 1011.84 530 similar to peptidylprolyl isomerase a (cyclophilin a); cyclophilin-lc; cyclophilin homolog overexpressed in liver cancer; chromosome 1 amplified sequence 2. [refseq;acc:nm_178230]
1.05538 958.732 1011.83 527 keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]
958.748 1011.84 528 keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]
958.749 529 star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]
1.05539 958.724 1011.83 523 keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]
958.726 524 keratin associated protein 1.5. [refseq;acc:nm_031957]
525 keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]
958.728 522 keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]
526 keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]
1.05571 2864.68 High confidence 2713.5 373 kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]
1.05582 2192.97 Low confidence 2077.04 521 zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]
1.05585 402.138 380.866 520 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]
958.097 1011.61 519 keratin associated protein 9.2. [refseq;acc:nm_031961]
1.05639 1279.26 1351.4 518 cytochrome c oxidase subunit viia-l related protein, mitochondrial precursor. [swissprot;acc:o60397]
1.0566 1311.25 1385.47 517 transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690]
1.05726 3920.97 3708.61 516 60s ribosomal protein l18a. [swissprot;acc:q02543]
1.05755 1134.29 1199.57 515 ba371l19.2 (novel protein similar to 40s ribosomal protein s10 (rps10)). [sptrembl;acc:q9nq39]
1.05771 16295.1 17235.5 514 rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565]
1.05782 5130.58 High confidence 5427.25 372 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]
1.05788 1135.73 Low confidence 1201.47 513 40s ribosomal protein s10. [swissprot;acc:p46783]
1.05818 2837.61 3002.7 512 brain protein 16. [refseq;acc:nm_016458]
1.05819 1542.23 High confidence 1631.97 371 phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6]
1.05827 3631.3 Low confidence 3842.88 511 p28 ing5. [refseq;acc:nm_032329]
1.05861 2837.1 2680.03 510 dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]
1.05865 4610.93 4881.38 509 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]
1.05868 1951.18 2065.68 508 ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]
1.05888 779.665 825.575 507 pr-domain zinc finger protein 7. [swissprot;acc:q9nqw5]
1.05913 2301.01 2437.08 506 dead-box protein 3, y-chromosomal. [swissprot;acc:o15523]
1.05922 1913.73 2027.06 505 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]
1.05959 569 537 504 g protein pathway suppressor 2 (gps2 protein). [swissprot;acc:q13227]
1.05962 1895.34 1788.69 503 60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268]
1.05969 5516.84 5846.15 502 baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]
1.05977 1225.02 1298.24 501 rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513]
1.05986 2814.85 2983.35 500 phosphoinositide-3-kinase, regulatory subunit 4, p150; phosphatidylinositol 3-kinase-associated p150. [refseq;acc:nm_014602]
1.05992 1585.99 1681.03 499 dj422b11.1.1 (dna primase large subunit (polypeptide 2a, p58)) (fragment). [sptrembl;acc:q9h412]
1.06023 1010.2 952.812 498 solute carrier family 4, sodium bicarbonate cotransporter, member 8. [refseq;acc:nm_004858]

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/