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 measured Gene expected description Hugo final
Results: HTML CSV LaTeX Showing element 302 to 351 of 3206 in total
Rank
measured
expected
description
Hugo
final
302 0.515003 1.71949 ATG16L1 0.299509157
303 0.20849 0.697153 HPAII TINY FRAGMENTS LOCUS 9C. [RefSeq;Acc:NM_022727] no value 0.299059174
304 0.241123 0.807018 UBIQUITIN. [SWISSPROT;Acc:P02248] 0.298782679
305 0.329649 1.10466 ATG16L2 0.298416707
306 0.232016 0.784548 ALPHA-1-ACID GLYCOPROTEIN 2 PRECURSOR (AGP 2) (OROSOMUCOID 2) (OMD 2). [SWISSPROT;Acc:P19652] no value 0.295732065
307 0.0503334 0.170278 MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2B (MAD2-LIKE 2) (HREV7). [SWISSPROT;Acc:Q9UI95] MAD2L2 0.295595438
308 MITOCHONDRIAL 28S RIBOSOMAL PROTEIN S32 (S32MT) (MRP-S32) (PTD007) (HSPC204). [SWISSPROT;Acc:Q9Y6G3] no value
309 RBM42
310 0.251667 0.851392 NUCLEAR PORE COMPLEX PROTEIN NUP88 (NUCLEOPORIN NUP88) (88 KDA NUCLEAR PORE COMPLEX PROTEIN). [SWISSPROT;Acc:Q99567] NUP88 0.295594744
311 0.287802 0.973671 UBIQUITIN. [SWISSPROT;Acc:P02248] UBB 0.295584443
312 0.486534 1.64947 U2 SMALL NUCLEAR RIBONUCLEOPROTEIN A' (U2 SNRNP-A'). [SWISSPROT;Acc:P09661] SNRPA1 0.294963837
313 0.482398 1.63545 BA395L14.12 (NOVEL PROTEIN SIMILAR TO SMALL NUCLEAR RIBONUCLEOPROTEIN POLYPEPTIDE A' (SNRPA1)). [SPTREMBL;Acc:Q9NU36] no value 0.294963466
314 0.0820629 0.278835 PROTEIN CGI-147. [SWISSPROT;Acc:Q9Y3E5] PTRH2 0.29430631
315 0.120354 0.409455 SPLICEOSOMAL U5 SNRNP-SPECIFIC 15 KDA PROTEIN (DIM1 PROTEIN HOMOLOG) (THIOREDOXIN-LIKE U5 SNRNP PROTEIN U5-15KD). [SWISSPROT;Acc:O14834] TXNL4A 0.293937063
316 0.0933039 0.319772 SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN (SRP9). [SWISSPROT;Acc:P49458] SRP9 0.291782583
317 0.0750779 0.257511 0.291552206
318 0.0924045 0.317178 COLORECTAL MUTANT CANCER PROTEIN (MCC PROTEIN). [SWISSPROT;Acc:P23508] MCC 0.291333258
319 0.515195 1.77067 PRE-MRNA PROCESSING FACTOR 31 HOMOLOG; PRE-MRNA PROCESSING FACTOR 31 HOMOLOG (YEAST). [RefSeq;Acc:NM_015629] PRPF31 0.290960484
320 0.398804 1.37218 TUFTELIN-INTERACTING PROTEIN 11 (HSPC006). [SWISSPROT;Acc:Q9UBB9] TFIP11 0.290635339
321 0.102544 0.354268 KY 0.289453182
322 0.255373 0.886465 "HIGH-MOBILITY GROUP 20B; SOX-LIKE TRANSCRIPTIONAL FACTOR; SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY E, MEMBER 1-RELATED. [RefSeq;Acc:NM_006339]" HMG20B 0.288080184
323 0.176498 0.613112 THOC7 0.287872363
324 0.214269 0.744947 HIGH-MOBILITY GROUP 20A. [RefSeq;Acc:NM_018200] HMG20A 0.287629858
325 0.261495 0.912016 TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE (TER ATPASE) (15S MG(2+)- ATPASE P97 SUBUNIT) (VALOSIN CONTAINING PROTEIN) (VCP) [CONTAINS: VALOSIN]. [SWISSPROT;Acc:P55072] VCP 0.286721943
326 0.709304 2.4753 "PLEIOTROPIC REGULATOR 1 (PRL1HOMOLOG, ARABIDOPSIS); PLEIOTROPIC REGULATOR 1 (PRL1, ARABIDOPSIS HOMOLOG). [RefSeq;Acc:NM_002669]" PLRG1 0.286552741
327 0.10034 0.351521 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 4 (EC 2.7.1.-) (MAP KINASE KINASE 4) (JNK ACTIVATING KINASE 1) (C-JUN N- TERMINAL KINASE KINASE 1) (JNKK) (SAPK/ERK KINASE 1) (SEK1). [SWISSPROT;Acc:P45985] MAP2K4 0.285445251
328 0.0946713 0.331704 PEROXIREDOXIN 4 (EC 1.11.1.-) (PRX-IV) (THIOREDOXIN PEROXIDASE AO372) (THIOREDOXIN-DEPENDENT PEROXIDE REDUCTASE A0372) (ANTIOXIDANT ENZYME AOE372) (AOE37-2). [SWISSPROT;Acc:Q13162] PRDX4 0.285408979
329 0.228764 0.80202 L-MYC-1 PROTO-ONCOGENE PROTEIN. [SWISSPROT;Acc:P12524] MYCL1 0.285234782
330 0.238906 0.837663 N-MYC PROTO-ONCOGENE PROTEIN. [SWISSPROT;Acc:P04198] MYCN 0.285205387
331 0.133623 0.468587 GA BINDING PROTEIN ALPHA CHAIN (GABP-ALPHA SUBUNIT) (TRANSCRIPTION FACTOR E4TF1-60) (NUCLEAR RESPIRATORY FACTOR-2 SUBUNIT ALPHA). [SWISSPROT;Acc:Q06546] GABPA 0.28516156
332 0.0963108 0.337743 "NADH-UBIQUINONE OXIDOREDUCTASE 23 KDA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-23KD) (CI-23KD) (TYKY SUBUNIT). [SWISSPROT;Acc:O00217]" NDUFS8 0.285160018
333 0.0373117 0.130845 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] no value 0.28515954
334 0.0756863 0.265419 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 1 (CGI-88). [SWISSPROT;Acc:Q9BW60] ELOVL1 0.285157807
335 0.304036 1.06655 MYC PROTO-ONCOGENE PROTEIN (C-MYC). [SWISSPROT;Acc:P01106] MYC 0.285064929
336 0.216233 0.758752 HISTONE ACETYLTRANSFERASE TYPE B SUBUNIT 2 (RETINOBLASTOMA BINDING PROTEIN P46) (RETINOBLASTOMA-BINDING PROTEIN 7) (RBBP-7). [SWISSPROT;Acc:Q16576] RBBP7 0.284985081
337 0.555029 1.94761 M-PHASE INDUCER PHOSPHATASE 1 (EC 3.1.3.48) (DUAL SPECIFICITY PHOSPHATASE CDC25A). [SWISSPROT;Acc:P30304] CDC25A 0.284979539
338 0.091005 0.319446 METASTASIS-ASSOCIATED PROTEIN MTA1. [SWISSPROT;Acc:Q13330] MTA1 0.28488383
339 0.894103 3.13898 SPLICING FACTOR 3 SUBUNIT 1 (SPLICEOSOME ASSOCIATED PROTEIN 114) (SAP 114) (SF3A120). [SWISSPROT;Acc:Q15459] SF3A1 0.284838706
340 0.0420473 0.147618 SPLICING FACTOR 3A SUBUNIT 3 (SPLICEOSOME ASSOCIATED PROTEIN 61) (SAP 61) (SF3A60). [SWISSPROT;Acc:Q12874] SF3A3 0.28483857
341 0.232195 0.815319 CHROMATIN ASSEMBLY FACTOR 1 SUBUNIT C (CAF-1 SUBUNIT C) (CHROMATIN ASSEMBLY FACTOR I P48 SUBUNIT) (CAF-I 48 KDA SUBUNIT) (CAF-IP48) (RETINOBLASTOMA BINDING PROTEIN P48) (RETINOBLASTOMA-BINDING PROTEIN 4) (RBBP-4) (MSI1 PROTEIN HOMOLOG). [SWISSPROT; RBBP4 0.28479037
342 0.137665 0.484315 DYSTROBREVIN BINDING PROTEIN 1; DYSBINDIN. [RefSeq;Acc:NM_032122] DTNBP1 0.284246823
343 0.0396993 0.139829 C16orf57 0.283913208
344 0.71417 2.51546 NUCLEAR MATRIX PROTEIN NMP200 RELATED TO SPLICING FACTOR PRP19. [RefSeq;Acc:NM_014502] PRPF19 0.283912286
345 1.799 6.36689 ALPHA-ACTININ 2 (ALPHA ACTININ SKELETAL MUSCLE ISOFORM 2) (F-ACTIN CROSS LINKING PROTEIN). [SWISSPROT;Acc:P35609] ACTN2 0.282555533
346 0.1052 0.372425 DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1B (EC 2.7.1.-) (MIRK PROTEIN KINASE). [SWISSPROT;Acc:Q9Y463] DYRK1B 0.282472981
347 0.135144 0.478436 no value 0.282470383
348 DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A (EC 2.7.1.-) (PROTEIN KINASE MINIBRAIN HOMOLOG) (MNBH) (HP86) (DUAL SPECIFICITY YAK1-RELATED KINASE). [SWISSPROT;Acc:Q13627] DYRK1A
349 ELONGATION PROTEIN 4 HOMOLOG; PAX6 NEIGHBOR GENE; CHROMOSOME 11 OPEN READING FRAME 19. [RefSeq;Acc:NM_019040] ELP4
350 0.116954 0.41404 MAPKBP1 0.282470293
351 1.53732 5.44319 ALPHA-ACTININ 1 (ALPHA-ACTININ CYTOSKELETAL ISOFORM) (NON-MUSCLE ALPHA-ACTININ 1) (F-ACTIN CROSS LINKING PROTEIN). [SWISSPROT;Acc:P12814] ACTN1 0.282429972

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/