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 352 to 401 of 3206 in total
Rank
description
measured
expected
final
Hugo
352 ALPHA-ACTININ 4 (NON-MUSCLE ALPHA-ACTININ 4) (F-ACTIN CROSS LINKING PROTEIN). [SWISSPROT;Acc:O43707] 1.5119 5.35346 0.282415485 ACTN4
353 TRANSCRIPTION INITIATION FACTOR TFIID 55 KDA SUBUNIT (TAFII-55) (TAFII55). [SWISSPROT;Acc:Q15545] 0.124527 0.441415 0.282108673 TAF7
354 "TATA BOX BINDING PROTEIN-ASSOCIATED FACTOR, RNA POLYMERASE II, Q; TAF7-LIKE RNA POLYMERASE II, TATA BOX BINDING PROTEIN (TBP)-ASSOCIATED FACTOR, 50 KD; TBP-ASSOCIATED FACTOR, RNA POLYMERASE II, Q. [RefSeq;Acc:NM_024885]" 0.103996 0.36903 0.281809067 TAF7L
355 EXOCYST COMPLEX COMPONENT SEC15B. [SWISSPROT;Acc:Q9Y2D4] 0.117602 0.417668 0.281568135 EXOC6B
356 0.0483186 0.171674 0.281455549 no value
357 0.042516 0.151058 0.281454805
358 PROTEIN AD-016 (PROTEIN CGI-116) (X0009). [SWISSPROT;Acc:Q9Y3C0] 0.3145 1.11741 0.281454435 CCDC53
359 "CLEAVAGE AND POLYADENYLATION SPECIFIC FACTOR 5, 25 KD SUBUNIT; PRE-MRNA CLEAVAGE FACTOR IM (25KD); PRE-MRNA CLEAVAGE FACTOR IM, 25KD SUBUNIT. [RefSeq;Acc:NM_007006]" 0.288916 1.0267 0.281402552 NUDT21
360 EXOCYST COMPLEX COMPONENT SEC15A. [SWISSPROT;Acc:Q8TAG9] 0.138286 0.49236 0.280863596 EXOC6
361 EXOCYST COMPLEX COMPONENT SEC8. [SWISSPROT;Acc:Q96A65] 0.090885 0.324189 0.280345724 EXOC4
362 OSTEOCLAST STIMULATING FACTOR 1. [SWISSPROT;Acc:Q92882] 0.0741822 0.264688 0.2802628 OSTF1
363 SPLICING FACTOR 3B SUBUNIT 4 (SPLICEOSOME ASSOCIATED PROTEIN 49) (SAP 49) (SF3B50) (PRE-MRNA SPLICING FACTOR SF3B 49 KDA SUBUNIT). [SWISSPROT;Acc:Q15427] 0.0893365 0.318821 0.280208957 SF3B4
364 "C316G12.2 (NOVEL PROTEIN SIMILAR TO PREDICTED YEAST, WORM AND ARCHAE- BACTERIAL PROTEINS) (SIMILAR TO UND313) (S. CERVISIAE) (HYPOTHETICAL PROTEIN). [SPTREMBL;Acc:Q9UJK0]" 0.131623 0.469919 0.280097208 C16orf42
365 G-RICH SEQUENCE FACTOR-1 (GRSF-1). [SWISSPROT;Acc:Q12849] 0.170665 0.610067 0.279747962 GRSF1
366 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN H3 (HNRNP H3) (HNRNP 2H9). [SWISSPROT;Acc:P31942] 0.179445 0.641462 0.279743773 HNRPH3
367 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN F (HNRNP F). [SWISSPROT;Acc:P52597] 0.198738 0.710442 0.279738529 HNRPF
368 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN H (HNRNP H). [SWISSPROT;Acc:P31943] 0.219762 0.785612 0.279733507 HNRPH1
369 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN H' (HNRNP H') (FTP-3). [SWISSPROT;Acc:P55795] 0.222111 0.794014 0.279731844 HNRPH2
370 "COFILIN, NON-MUSCLE ISOFORM (18 KDA PHOSPHOPROTEIN) (P18). [SWISSPROT;Acc:P23528]" 0.0460179 0.164816 0.279207723 CFL1
371 DESTRIN (ACTIN-DEPOLYMERIZING FACTOR) (ADF). [SWISSPROT;Acc:P18282] DSTN
372 "COFILIN, MUSCLE ISOFORM (COFILIN 2). [SWISSPROT;Acc:Q9Y281]" CFL2
373 0.034272 0.122748 0.279206179 no value
374 UBIQUITIN FUSION DEGRADATION PROTEIN 1 HOMOLOG (UB FUSION PROTEIN 1). [SWISSPROT;Acc:Q92890] 0.379312 1.35854 0.279205618 UFD1L
375 "DYNEIN INTERMEDIATE CHAIN 2, CYTOSOLIC (DH IC-2) (CYTOPLASMIC DYNEIN INTERMEDIATE CHAIN 2). [SWISSPROT;Acc:Q13409]" 0.119541 0.428154 0.279200942 DYNC1I2
376 PRE-MRNA SPLICING FACTOR PRP17 (HPRP17) (EH-BINDING PROTEIN 3) (EHB3). [SWISSPROT;Acc:O60508] 0.274292 0.982579 0.279155162 CDC40
377 0.0389719 0.139616 0.279136345 CCDC12
378 PTB DOMAIN ADAPTOR PROTEIN CED-6; ENGULFMENT ADAPTER PROTEIN. [RefSeq;Acc:NM_016315] 0.0573826 0.205572 0.279136264 GULP1
379 CROOKED NECK-LIKE PROTEIN 1 (CROOKED NECK HOMOLOG) (HCRN) (CGI-201) (MSTP021). [SWISSPROT;Acc:Q9BZJ0] 0.802935 2.8765 0.279136103 CRNKL1
380 CALCYPHOSINE. [SWISSPROT;Acc:Q13938] 0.0480742 0.172225 0.279136014 CAPS
381 0.0666911 0.23892 0.279135694 CAPSL
382 MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG (MITOCHONDRIAL 20 KDA OUTER MEMBRANE PROTEIN) (OUTER MITOCHONDRIAL MEMBRANE RECEPTOR TOM20). [SWISSPROT;Acc:Q15388] 0.0530069 0.189914 0.279110018 TOMM20
383 PEROXISOMAL FARNESYLATED PROTEIN (33 KDA HOUSEKEEPING PROTEIN) (PEROXIN 19). [SWISSPROT;Acc:P40855] 0.245859 0.88087 0.27910929 PEX19
384 CDC42-INTERACTING PROTEIN 4 (THYROID RECEPTOR INTERACTING PROTEIN 10) (TRIP-10). [SWISSPROT;Acc:Q15642] 0.448126 1.60594 0.279042804 TRIP10
385 "DYNEIN INTERMEDIATE CHAIN 1, CYTOSOLIC (DH IC-1) (CYTOPLASMIC DYNEIN INTERMEDIATE CHAIN 1). [SWISSPROT;Acc:O14576]" 0.104222 0.373698 0.278893652 DYNC1I1
386 "GRPE PROTEIN HOMOLOG 2, MITOCHONDRIAL PRECURSOR (MT-GRPE#2). [SWISSPROT;Acc:Q8TAA5]" 0.0678064 0.243254 0.278747318 GRPEL2
387 "GRPE PROTEIN HOMOLOG 1, MITOCHONDRIAL PRECURSOR (MT-GRPE#1) (HMGE). [SWISSPROT;Acc:Q9HAV7]" 0.0851715 0.305551 0.278747247 GRPEL1
388 "SWI/SNF RELATED, MATRIX ASSOCIATED, ACTIN DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY D MEMBER 1 (SWI/SNF COMPLEX 60 KDA SUBUNIT) (BRG1- ASSOCIATED FACTOR 60A). [SWISSPROT;Acc:Q96GM5]" 0.140567 0.504282 0.278746812 SMARCD1
389 SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN D2; RSC6P; MAMMALIAN CHROMATIN REMODELING COMPLEX BRG1-ASSOCIATED FACTOR 60B; SWP73-LIKE PROTEIN; CHROMATIN REMODELING COMPLEX BAF60B SUBUNIT; SWI/SNF COMPLEX 60 KDA SUBUNIT B. [Sour 0.0474703 0.170299 0.278746792 SMARCD2
390 SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN D3; RSC6P; MAMMALIAN CHROMATIN REMODELING COMPLEX BRG1-ASSOCIATED FACTOR 60C; SWP73-LIKE PROTEIN; CHROMATIN REMODELING COMPLEX BAF60C SUBUNIT; SWI/SNF COMPLEX 60 KDA SUBUNIT C. [Sour 0.123465 0.44293 0.278746077 SMARCD3
391 0.368426 1.32182 0.278726302 FNBP1L
392 40S RIBOSOMAL PROTEIN S26. [SWISSPROT;Acc:P02383] 0.135061 0.484774 0.278606113 no value
393 MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM22. [SWISSPROT;Acc:Q9Y584] 0.0993399 0.356562 0.278604843 TIMM22
394 ATP SYNTHASE MITOCHONDRIAL F1 COMPLEX ASSEMBLY FACTOR 2. [RefSeq;Acc:NM_145691] ATPAF2
395 UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KDA PROTEIN (EC 1.10.2.2) (COMPLEX III SUBUNIT VI) (QP-C). [SWISSPROT;Acc:P14927] UQCRB
396 0.0370257 0.132897 0.278604483 TSR2
397 NHP2-LIKE PROTEIN 1 (HIGH MOBILITY GROUP-LIKE NUCLEAR PROTEIN 2 HOMOLOG 1) ([U4/U6.U5] TRI-SNRNP 15.5 KDA PROTEIN) (OTK27). [SWISSPROT;Acc:P55769] 0.0337208 0.121119 0.278410489 NHP2L1
398 NUCLEAR FRAGILE X MENTAL RETARDATION PROTEIN INTERACTING PROTEIN 1; NUCLEAR FRAGILE X MENTAL RETARDATION INTERCATING PROTEIN 1; NUCLEAR FRAGILE X MENTAL RETARDATION PROTEIN-INTERACTING PROTEIN 1. [RefSeq;Acc:NM_012345] 0.0673151 0.241784 0.278410068 NUFIP1
399 THYROID RECEPTOR INTERACTING PROTEIN 3 (TRIP-3) (FRAGMENT). [SWISSPROT;Acc:Q15649] 0.0671887 0.24133 0.278410061 ZNHIT3
400 TRANSCRIPTION INITIATION FACTOR IIB (GENERAL TRANSCRIPTION FACTOR TFIIB) (S300-II). [SWISSPROT;Acc:Q00403] 0.101036 0.362904 0.278409717 GTF2B
401 M-PHASE INDUCER PHOSPHATASE 3 (EC 3.1.3.48) (DUAL SPECIFICITY PHOSPHATASE CDC25C). [SWISSPROT;Acc:P30307] 0.590395 2.12136 0.278309669 CDC25C

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/