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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene expected description measured final Hugo
Results: HTML CSV LaTeX Showing element 302 to 351 of 3206 in total
Rank
expected
description
measured
final
Hugo
302 1.71949 0.515003 0.299509157 ATG16L1
303 0.697153 HPAII TINY FRAGMENTS LOCUS 9C. [RefSeq;Acc:NM_022727] 0.20849 0.299059174 no value
304 0.807018 UBIQUITIN. [SWISSPROT;Acc:P02248] 0.241123 0.298782679
305 1.10466 0.329649 0.298416707 ATG16L2
306 0.784548 ALPHA-1-ACID GLYCOPROTEIN 2 PRECURSOR (AGP 2) (OROSOMUCOID 2) (OMD 2). [SWISSPROT;Acc:P19652] 0.232016 0.295732065 no value
307 0.170278 MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2B (MAD2-LIKE 2) (HREV7). [SWISSPROT;Acc:Q9UI95] 0.0503334 0.295595438 MAD2L2
308 MITOCHONDRIAL 28S RIBOSOMAL PROTEIN S32 (S32MT) (MRP-S32) (PTD007) (HSPC204). [SWISSPROT;Acc:Q9Y6G3] no value
309 RBM42
310 0.851392 NUCLEAR PORE COMPLEX PROTEIN NUP88 (NUCLEOPORIN NUP88) (88 KDA NUCLEAR PORE COMPLEX PROTEIN). [SWISSPROT;Acc:Q99567] 0.251667 0.295594744 NUP88
311 0.973671 UBIQUITIN. [SWISSPROT;Acc:P02248] 0.287802 0.295584443 UBB
312 1.64947 U2 SMALL NUCLEAR RIBONUCLEOPROTEIN A' (U2 SNRNP-A'). [SWISSPROT;Acc:P09661] 0.486534 0.294963837 SNRPA1
313 1.63545 BA395L14.12 (NOVEL PROTEIN SIMILAR TO SMALL NUCLEAR RIBONUCLEOPROTEIN POLYPEPTIDE A' (SNRPA1)). [SPTREMBL;Acc:Q9NU36] 0.482398 0.294963466 no value
314 0.278835 PROTEIN CGI-147. [SWISSPROT;Acc:Q9Y3E5] 0.0820629 0.29430631 PTRH2
315 0.409455 SPLICEOSOMAL U5 SNRNP-SPECIFIC 15 KDA PROTEIN (DIM1 PROTEIN HOMOLOG) (THIOREDOXIN-LIKE U5 SNRNP PROTEIN U5-15KD). [SWISSPROT;Acc:O14834] 0.120354 0.293937063 TXNL4A
316 0.319772 SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN (SRP9). [SWISSPROT;Acc:P49458] 0.0933039 0.291782583 SRP9
317 0.257511 0.0750779 0.291552206
318 0.317178 COLORECTAL MUTANT CANCER PROTEIN (MCC PROTEIN). [SWISSPROT;Acc:P23508] 0.0924045 0.291333258 MCC
319 1.77067 PRE-MRNA PROCESSING FACTOR 31 HOMOLOG; PRE-MRNA PROCESSING FACTOR 31 HOMOLOG (YEAST). [RefSeq;Acc:NM_015629] 0.515195 0.290960484 PRPF31
320 1.37218 TUFTELIN-INTERACTING PROTEIN 11 (HSPC006). [SWISSPROT;Acc:Q9UBB9] 0.398804 0.290635339 TFIP11
321 0.354268 0.102544 0.289453182 KY
322 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]" 0.255373 0.288080184 HMG20B
323 0.613112 0.176498 0.287872363 THOC7
324 0.744947 HIGH-MOBILITY GROUP 20A. [RefSeq;Acc:NM_018200] 0.214269 0.287629858 HMG20A
325 0.912016 TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE (TER ATPASE) (15S MG(2+)- ATPASE P97 SUBUNIT) (VALOSIN CONTAINING PROTEIN) (VCP) [CONTAINS: VALOSIN]. [SWISSPROT;Acc:P55072] 0.261495 0.286721943 VCP
326 2.4753 "PLEIOTROPIC REGULATOR 1 (PRL1HOMOLOG, ARABIDOPSIS); PLEIOTROPIC REGULATOR 1 (PRL1, ARABIDOPSIS HOMOLOG). [RefSeq;Acc:NM_002669]" 0.709304 0.286552741 PLRG1
327 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] 0.10034 0.285445251 MAP2K4
328 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] 0.0946713 0.285408979 PRDX4
329 0.80202 L-MYC-1 PROTO-ONCOGENE PROTEIN. [SWISSPROT;Acc:P12524] 0.228764 0.285234782 MYCL1
330 0.837663 N-MYC PROTO-ONCOGENE PROTEIN. [SWISSPROT;Acc:P04198] 0.238906 0.285205387 MYCN
331 0.468587 GA BINDING PROTEIN ALPHA CHAIN (GABP-ALPHA SUBUNIT) (TRANSCRIPTION FACTOR E4TF1-60) (NUCLEAR RESPIRATORY FACTOR-2 SUBUNIT ALPHA). [SWISSPROT;Acc:Q06546] 0.133623 0.28516156 GABPA
332 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]" 0.0963108 0.285160018 NDUFS8
333 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] 0.0373117 0.28515954 no value
334 0.265419 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 1 (CGI-88). [SWISSPROT;Acc:Q9BW60] 0.0756863 0.285157807 ELOVL1
335 1.06655 MYC PROTO-ONCOGENE PROTEIN (C-MYC). [SWISSPROT;Acc:P01106] 0.304036 0.285064929 MYC
336 0.758752 HISTONE ACETYLTRANSFERASE TYPE B SUBUNIT 2 (RETINOBLASTOMA BINDING PROTEIN P46) (RETINOBLASTOMA-BINDING PROTEIN 7) (RBBP-7). [SWISSPROT;Acc:Q16576] 0.216233 0.284985081 RBBP7
337 1.94761 M-PHASE INDUCER PHOSPHATASE 1 (EC 3.1.3.48) (DUAL SPECIFICITY PHOSPHATASE CDC25A). [SWISSPROT;Acc:P30304] 0.555029 0.284979539 CDC25A
338 0.319446 METASTASIS-ASSOCIATED PROTEIN MTA1. [SWISSPROT;Acc:Q13330] 0.091005 0.28488383 MTA1
339 3.13898 SPLICING FACTOR 3 SUBUNIT 1 (SPLICEOSOME ASSOCIATED PROTEIN 114) (SAP 114) (SF3A120). [SWISSPROT;Acc:Q15459] 0.894103 0.284838706 SF3A1
340 0.147618 SPLICING FACTOR 3A SUBUNIT 3 (SPLICEOSOME ASSOCIATED PROTEIN 61) (SAP 61) (SF3A60). [SWISSPROT;Acc:Q12874] 0.0420473 0.28483857 SF3A3
341 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; 0.232195 0.28479037 RBBP4
342 0.484315 DYSTROBREVIN BINDING PROTEIN 1; DYSBINDIN. [RefSeq;Acc:NM_032122] 0.137665 0.284246823 DTNBP1
343 0.139829 0.0396993 0.283913208 C16orf57
344 2.51546 NUCLEAR MATRIX PROTEIN NMP200 RELATED TO SPLICING FACTOR PRP19. [RefSeq;Acc:NM_014502] 0.71417 0.283912286 PRPF19
345 6.36689 ALPHA-ACTININ 2 (ALPHA ACTININ SKELETAL MUSCLE ISOFORM 2) (F-ACTIN CROSS LINKING PROTEIN). [SWISSPROT;Acc:P35609] 1.799 0.282555533 ACTN2
346 0.372425 DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1B (EC 2.7.1.-) (MIRK PROTEIN KINASE). [SWISSPROT;Acc:Q9Y463] 0.1052 0.282472981 DYRK1B
347 0.478436 0.135144 0.282470383 no value
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 0.41404 0.116954 0.282470293 MAPKBP1
351 5.44319 ALPHA-ACTININ 1 (ALPHA-ACTININ CYTOSKELETAL ISOFORM) (NON-MUSCLE ALPHA-ACTININ 1) (F-ACTIN CROSS LINKING PROTEIN). [SWISSPROT;Acc:P12814] 1.53732 0.282429972 ACTN1

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/