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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Rank Gene description measured final expected Hugo
Results: HTML CSV LaTeX Showing element 2508 to 2557 of 3206 in total
Rank
description
measured
final
expected
Hugo
2508 RAS SUPPRESSOR PROTEIN 1 (RSU-1) (RSP-1). [SWISSPROT;Acc:Q15404] 0.214312 0.214767522 0.997879 RSU1
2509 D(4) DOPAMINE RECEPTOR (D(2C) DOPAMINE RECEPTOR). [SWISSPROT;Acc:P21917] 0.0585879 0.214767391 0.272797 DRD4
2510 AMINOADIPATE-SEMIALDEHYDE SYNTHASE; LYSINE-KETOGLUTARATE REDUCTASE /SACCHAROPINE DEHYDROGENASE; LYSINE-2-OXOGLUTARATE REDUCTASE; AMINOADIPIC SEMIALDEHYDE SYNTHASE. [RefSeq;Acc:NM_005763] 0.0833117 0.214767372 0.387916 AASS
2511 0.0343037 0.214767256 0.159725 C20orf42
2512 INTEGRIN-LINKED PROTEIN KINASE 1 (EC 2.7.1.-) (ILK-1) (59 KDA SERINE/THREONINE PROTEIN KINASE) (P59ILK). [SWISSPROT;Acc:Q13418] 0.192216 0.2147672 0.894997 ILK
2513 PINCH PROTEIN (PARTICULARLY INTERESTING NEW CYS-HIS PROTEIN) (LIM AND SENESCENT CELL ANTIGEN-LIKE DOMAINS 1). [SWISSPROT;Acc:P48059] 0.113204 0.214767189 0.527101 LIMS1
2514 LIM AND SENESCENT CELL ANTIGEN-LIKE DOMAINS 2; ILK-BINDING PROTEIN. [RefSeq;Acc:NM_017980] 0.117844 0.214767107 0.548706 LIMS2
2515 ESPIN. [RefSeq;Acc:NM_031475] 0.0601277 0.214767098 0.279967 ESPNP
2516 STAR-RELATED LIPID TRANSFER PROTEIN 5 (STARD5) (START DOMAIN- CONTAINING PROTEIN 5). [SWISSPROT;Acc:Q9NSY2] 0.0598238 0.214767081 0.278552 STARD5
2517 C11orf46
2518 RAS-GTPASE-ACTIVATING PROTEIN BINDING PROTEIN 2 (GAP SH3-DOMAIN BINDING PROTEIN 2) (G3BP-2). [SWISSPROT;Acc:Q9UN86] G3BP2
2519 RAS-GTPASE-ACTIVATING PROTEIN BINDING PROTEIN 1 (GAP SH3-DOMAIN BINDING PROTEIN 1) (G3BP-1). [SWISSPROT;Acc:Q13283] 0.0506049 0.214766983 0.235627 G3BP1
2520 CYTOCHROME P450 2D6 (EC 1.14.14.1) (CYPIID6) (P450-DB1) (DEBRISOQUINE 4-HYDROXYLASE). [SWISSPROT;Acc:P10635] 0.0555486 0.214766901 0.258646 CYP2D6
2521 KERATIN ASSOCIATED PROTEIN 4-12; KERATIN ASSOCIATED PROTEIN 4.12. [RefSeq;Acc:NM_031854] 0.042399 0.214765475 0.19742 no value
2522 0.0436957 0.21476521 0.203458
2523 STAR-RELATED LIPID TRANSFER PROTEIN 4 (STARD4) (START DOMAIN- CONTAINING PROTEIN 4). [SWISSPROT;Acc:Q96DR4] 0.0433512 0.214765127 0.201854 STARD4
2524 STAR-RELATED LIPID TRANSFER PROTEIN 6 (STARD6) (START DOMAIN- CONTAINING PROTEIN 6). [SWISSPROT;Acc:P59095] 0.043878 0.214765035 0.204307 STARD6
2525 KERATIN ASSOCIATED PROTEIN 4.9 (FRAGMENT). [SPTREMBL;Acc:Q9BYQ8] 0.0383264 0.214764258 0.178458 no value
2526 KERATIN ASSOCIATED PROTEIN 4-14; KERATIN ASSOCIATED PROTEIN 4.14. [RefSeq;Acc:NM_033059] 0.0382656 0.214764136 0.178175
2527 KERATIN ASSOCIATED PROTEIN 4.4. [RefSeq;Acc:NM_032524] 0.0320251 0.214763476 0.149118 KRTAP4-4
2528 KERATIN ASSOCIATED PROTEIN 4-2; KERATIN ASSOCIATED PROTEIN 4.2. [RefSeq;Acc:NM_033062] 0.0314375 0.21476196 0.146383 no value
2529 KERATIN ASSOCIATED PROTEIN 4-10; KERATIN ASSOCIATED PROTEIN 4.10. [RefSeq;Acc:NM_033060] 0.0280741 0.214761861 0.130722
2530 "KERATIN, ULTRA HIGH-SULFUR MATRIX PROTEIN A (UHS KERATIN A) (UHS KERA). [SWISSPROT;Acc:P26371]" 0.0250957 0.214761155 0.116854
2531 KERATIN ASSOCIATED PROTEIN 1-3; KERATIN ASSOCIATED PROTEIN 1.3. [RefSeq;Acc:NM_030966] 0.0258656 0.214760999 0.120439
2532 KERATIN ASSOCIATED PROTEIN 1.5. [RefSeq;Acc:NM_031957] 0.0249741 0.214760766 0.116288
2533 KERATIN ASSOCIATED PROTEIN 2-4; KERATIN ASSOCIATED PROTEIN 2.4. [RefSeq;Acc:NM_033184] 0.0240826 0.214760516 0.112137
2534 KERATIN ASSOCIATED PROTEIN 4.3 (FRAGMENT). [SPTREMBL;Acc:Q9BYR4] 0.0260682 0.214759892 0.121383
2535 "KERATIN, ULTRA HIGH-SULFUR MATRIX PROTEIN B (UHS KERATIN B) (UHS KERB). [SWISSPROT;Acc:O75690]" 0.0249538 0.214759798 0.116194 KRTAP5-8
2536 ORNITHINE DECARBOXYLASE (EC 4.1.1.17) (ODC). [SWISSPROT;Acc:P11926] 0.220469 0.214737652 1.02669 ODC1
2537 "[3-METHYL-2-OXOBUTANOATE DEHYDROGENASE [LIPOAMIDE]] KINASE, MITOCHONDRIAL PRECURSOR (EC 2.7.1.115) (BRANCHED-CHAIN ALPHA-KETOACID DEHYDROGENASE KINASE) (BCKDHKIN) (BCKD-KINASE). [SWISSPROT;Acc:O14874]" 1.13737 0.21465603 5.29857 BCKDK
2538 DIPEPTIDYLPEPTIDASE 10; DIPEPTIDYL PEPTIDASE IV-RELATED PROTEIN 3. [RefSeq;Acc:NM_020868] 0.031831 0.214618984 0.148314 DPP10
2539 DIPEPTIDYL AMINOPEPTIDASE-LIKE PROTEIN 6 (DIPEPTIDYLPEPTIDASE VI) (DIPEPTIDYLPEPTIDASE 6) (DIPEPTIDYL PEPTIDASE IV LIKE PROTEIN) (DIPEPTIDYL AMINOPEPTIDASE-RELATED PROTEIN) (DPPX). [SWISSPROT;Acc:P42658] 0.0311751 0.214618816 0.145258 DPP6
2540 SEPRASE (EC 3.4.21.-) (FIBROBLAST ACTIVATION PROTEIN ALPHA) (INTEGRAL MEMBRANE SERINE PROTEASE) (170-KDA MELANOMA MEMBRANE-BOUND GELATINASE). [SWISSPROT;Acc:Q12884] 0.0377549 0.214616469 0.175918 FAP
2541 0.0217565 0.214614057 0.101375 no value
2542 SURFEIT LOCUS PROTEIN 1. [SWISSPROT;Acc:Q15526] 0.12372 0.214613939 0.576477 SURF1
2543 0.0209707 0.214613494 0.0977138 FAM86C
2544 COX15 HOMOLOG ISOFORM 2 PRECURSOR; CYTOCHROME C OXIDASE SUBUNIT 15; CYTOCHROME C OXIDASE ASSEMBLY PROTEIN. [RefSeq;Acc:NM_004376] 0.0273323 0.214613367 0.127356 COX15
2545 FAM86B2
2546 "CYTOCHROME C OXIDASE ASSEMBLY PROTEIN COX11, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:Q9Y6N1]" 0.124724 0.214613263 0.581157 COX11
2547 "PROTOHEME IX FARNESYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.5.1.-) (HEME O SYNTHASE). [SWISSPROT;Acc:Q12887]" 0.0819968 0.214613106 0.382068 COX10
2548 KERATIN ASSOCIATED PROTEIN 9.2. [RefSeq;Acc:NM_031961] 1.11949 0.214609693 5.2164 KRTAP9-8
2549 "[PYRUVATE DEHYDROGENASE [LIPOAMIDE]] KINASE ISOZYME 2, MITOCHONDRIAL PRECURSOR (EC 2.7.1.99) (PYRUVATE DEHYDROGENASE KINASE ISOFORM 2). [SWISSPROT;Acc:Q15119]" 0.845658 0.214584993 3.9409 PDK2
2550 "[PYRUVATE DEHYDROGENASE [LIPOAMIDE]] KINASE ISOZYME 1, MITOCHONDRIAL PRECURSOR (EC 2.7.1.99) (PYRUVATE DEHYDROGENASE KINASE ISOFORM 1). [SWISSPROT;Acc:Q15118]" 0.844424 0.214584959 3.93515 PDK1
2551 "METHIONYL-TRNA FORMYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.2.9) (MTFMT). [SWISSPROT;Acc:Q96DP5]" 0.510943 0.214535904 2.38162 MTFMT
2552 "DNA TOPOISOMERASE II, ALPHA ISOZYME (EC 5.99.1.3). [SWISSPROT;Acc:P11388]" 0.286606 0.214480498 1.33628 no value
2553 0.0511995 0.214472422 0.238723
2554 "DNA TOPOISOMERASE II, BETA ISOZYME (EC 5.99.1.3). [SWISSPROT;Acc:Q02880]" 0.249175 0.214464001 1.16185 TOP2B
2555 METABOTROPIC GLUTAMATE RECEPTOR 3 PRECURSOR (MGLUR3). [SWISSPROT;Acc:Q14832] 0.0333153 0.214313835 0.155451 no value
2556 C1orf26
2557 METABOTROPIC GLUTAMATE RECEPTOR 2 PRECURSOR (MGLUR2). [SWISSPROT;Acc:Q14416] 0.0283513 0.214313359 0.132289 GRM2

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
- Hugo is the bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/