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