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 expected final Hugo
Results: HTML CSV LaTeX Showing element 1 to 50 of 350 in total
Hugo  : no value
Rank
description
measured
expected
final
4 3.66001 3.3348 1.097520091
17 0.0856348 0.180231 0.475139127
28 DOK-LIKE PROTEIN. [RefSeq;Acc:NM_024872] 0.0753031 0.176719 0.426117735
32 PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC (EC 2.7.1.112) (P60-SRC) (C-SRC). [SWISSPROT;Acc:P12931] 0.141847 0.33698 0.420935961
53 DISKS LARGE-ASSOCIATED PROTEIN 2 (DAP-2) (SAP90/PSD-95-ASSOCIATED PROTEIN 2) (SAPAP2) (PSD-95/SAP90 BINDING PROTEIN 2) (FRAGMENT). [SWISSPROT;Acc:Q9P1A6] 0.318849 0.775495 0.411155456
55 0.231369 0.562729 0.411155281
58 "DJ681N20.2 (NOVEL PROTEIN SIMILAR TO FERRITIN, LIGHT POLYPEPTIDE (FTL)). [SPTREMBL;Acc:Q9BYW6]" 0.0511645 0.124441 0.411154684
61 PUTATIVE ADENOSYLHOMOCYSTEINASE 3 (EC 3.3.1.1) (S-ADENOSYL-L- HOMOCYSTEINE HYDROLASE) (ADOHCYASE). [SWISSPROT;Acc:Q96HN2] 0.312681 0.760495 0.411154577
78 ASPARTATE BETA-HYDROXYLASE ISOFORM B; JUNCTIN ISOFORM 1; JUNCTATE; ASPARTYL/ASPARAGINYL-BETA-HYDROXYLASE; PEPTIDE-ASPARTATE BETA-DIOXYGENASE; HUMBUG. [RefSeq;Acc:NM_032468] 0.06383 0.157168 0.406125929
85 TRANSCRIPTION FACTOR DP-1 (E2F DIMERIZATION PARTNER 1) (DRTF1- POLYPEPTIDE-1) (DRTF1). [SWISSPROT;Acc:Q14186] 0.788778 2.02915 0.388723357
89 0.152828 0.396725 0.385224022
92 0.914796 2.37847 0.38461532
126 UBA/UBX 33.3 KDA PROTEIN. [SWISSPROT;Acc:Q04323] 0.375086 1.05643 0.3550505
127 ERO1-LIKE. [RefSeq;Acc:NM_014584] 0.0588477 0.165745 0.355049624
134 INTERLEUKIN-1 RECEPTOR-ASSOCIATED KINASE 4; INTERLEUKIN-1 RECEPTOR ASSOCIATED KINASE 4. [RefSeq;Acc:NM_016123] 0.290469 0.826637 0.351386401
159 FORMIN BINDING PROTEIN 3; FAS-LIGAND ASSOCIATED FACTOR 1; HUNTINGTIN-INTERACTING PROTEIN A; NY-REN-6 ANTIGEN. [RefSeq;Acc:NM_017892] 0.429285 1.22508 0.350413851
160 HUNTINGTIN-INTERACTING PROTEIN HYPA/FBP11 (FRAGMENT). [SPTREMBL;Acc:O75404] 0.40616 1.16002 0.350131894
178 FILAMIN A (ALPHA-FILAMIN) (FILAMIN 1) (ENDOTHELIAL ACTIN-BINDING PROTEIN) (ABP-280) (NONMUSCLE FILAMIN). [SWISSPROT;Acc:P21333] 0.0413389 0.122543 0.337341994
180 TRINUCLEOTIDE REPEAT CONTAINING 15. [RefSeq;Acc:NM_015575] 0.0561104 0.16661 0.336776904
213 RD PROTEIN. [SWISSPROT;Acc:P18615] 0.155654 0.485577 0.320554721
230 JUN DIMERIZATION PROTEIN. [RefSeq;Acc:NM_130469] 0.193648 0.614336 0.315215127
247 TRANSCRIPTION FACTOR BTF3 HOMOLOG 3. [SWISSPROT;Acc:Q13892] 0.625831 2.00343 0.312379769
249 NASCENT-POLYPEPTIDE-ASSOCIATED COMPLEX ALPHA POLYPEPTIDE. [RefSeq;Acc:NM_005594] 0.804734 2.57998 0.311914821
250 ALPHA-NAC PROTEIN. [SPTREMBL;Acc:Q9H009] 0.755644 2.42272 0.311899023
251 0.743299 2.38318 0.311893772
261 APOBEC-1 COMPLEMENTATION FACTOR ISOFORM 1; APOBEC-1 STIMULATING PROTEIN; APO-B RNA EDITING PROTEIN. [RefSeq;Acc:NM_014576] 0.0555455 0.180015 0.308560398
262 0.0556846 0.180466 0.308560061
263 RNA-BINDING PROTEIN. [RefSeq;Acc:NM_019027] 0.0560669 0.181705 0.308560029
267 0.152054 0.494121 0.307726245
269 SPLICING FACTOR 3B SUBUNIT 3 (SPLICEOSOME ASSOCIATED PROTEIN 130) (SAP 130) (SF3B130) (PRE-MRNA SPLICING FACTOR SF3B 130 KDA SUBUNIT). [SWISSPROT;Acc:Q15393] 1.08194 3.53138 0.306378809
287 "FATTY ACID-BINDING PROTEIN, EPIDERMAL (E-FABP) (PSORIASIS-ASSOCIATED FATTY ACID-BINDING PROTEIN HOMOLOG) (PA-FABP). [SWISSPROT;Acc:Q01469]" 0.0334849 0.110947 0.301809873
294 "BETA-CAROTENE DIOXYGENASE 2; PUTATIVE B,B-CAROTENE-9',10'-DIOXYGENASE. [RefSeq;Acc:NM_031938]" 0.0429558 0.142328 0.301808499
303 HPAII TINY FRAGMENTS LOCUS 9C. [RefSeq;Acc:NM_022727] 0.20849 0.697153 0.299059174
304 UBIQUITIN. [SWISSPROT;Acc:P02248] 0.241123 0.807018 0.298782679
306 ALPHA-1-ACID GLYCOPROTEIN 2 PRECURSOR (AGP 2) (OROSOMUCOID 2) (OMD 2). [SWISSPROT;Acc:P19652] 0.232016 0.784548 0.295732065
308 MITOCHONDRIAL 28S RIBOSOMAL PROTEIN S32 (S32MT) (MRP-S32) (PTD007) (HSPC204). [SWISSPROT;Acc:Q9Y6G3] 0.0503334 0.170278 0.295595438
313 BA395L14.12 (NOVEL PROTEIN SIMILAR TO SMALL NUCLEAR RIBONUCLEOPROTEIN POLYPEPTIDE A' (SNRPA1)). [SPTREMBL;Acc:Q9NU36] 0.482398 1.63545 0.294963466
333 GA BINDING PROTEIN BETA-2 CHAIN (GABP-BETA-2 SUBUNIT) (TRANSCRIPTION FACTOR E4TF1-47) (GAPBP-2) (NUCLEAR RESPIRATORY FACTOR-2 SUBUNIT GAMMA). [SWISSPROT;Acc:Q06545] 0.0373117 0.130845 0.28515954
347 0.135144 0.478436 0.282470383
356 0.0483186 0.171674 0.281455549
357 0.042516 0.151058 0.281454805
373 0.034272 0.122748 0.279206179
392 40S RIBOSOMAL PROTEIN S26. [SWISSPROT;Acc:P02383] 0.135061 0.484774 0.278606113
411 0.356784 1.28488 0.277678849
425 DEAD (ASP-GLU-ALA-ASP) BOX POLYPEPTIDE 47; HQP0256 PROTEIN. [RefSeq;Acc:NM_016355] 0.0884193 0.318777 0.277370387
438 TRANSFORMER-2 PROTEIN HOMOLOG (TRA-2 ALPHA). [SWISSPROT;Acc:Q13595] 0.345566 1.24774 0.276953532
452 "PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1 (EC 3.1.3.48) (PROTEIN-TYROSINE PHOSPHATASE 1B) (PTP-1B). [SWISSPROT;Acc:P18031]" 0.215243 0.779889 0.27599184
460 COLLAGEN ALPHA 5(IV) CHAIN PRECURSOR. [SWISSPROT;Acc:P29400] 0.0637349 0.231274 0.27558177699999997
492 0.0344618 0.125634 0.274303135
498 0.236585 0.862726 0.274229593

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/