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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expected Gene measured Rank Hugo description final
Results: HTML CSV LaTeX Showing element 2551 to 2600 of 3206 in total
expected
measured
Rank
Hugo
description
final
1.30706 0.299475 2076 PFDN5 PREFOLDIN SUBUNIT 5 (C-MYC BINDING PROTEIN MM-1) (MYC MODULATOR 1). [SWISSPROT;Acc:Q99471] 0.229121081
1.30736 0.223983 2918 PC "PYRUVATE CARBOXYLASE, MITOCHONDRIAL PRECURSOR (EC 6.4.1.1) (PYRUVIC CARBOXYLASE) (PCB). [SWISSPROT;Acc:P11498]" 0.171324654
1.30756 0.333664 984 TLE3 TRANSDUCIN-LIKE ENHANCER PROTEIN 3 (ESG3). [SWISSPROT;Acc:Q04726] 0.255180642
1.31793 0.299286 2165 no value 0.227087933
1.32007 0.349374 733 CTBP1 C-TERMINAL BINDING PROTEIN 1 (CTBP1). [SWISSPROT;Acc:Q13363] 0.264663238
1.32025 0.294007 2275 no value 0.2226904
1.32095 0.305347 1970 RPS9 40S RIBOSOMAL PROTEIN S9. [SWISSPROT;Acc:P46781] 0.231157122
1.3211 0.13205 3077 HOMER3 "HOMER, NEURONAL IMMEDIATE EARLY GENE, 3. [RefSeq;Acc:NM_004838]" 0.099954583
1.32182 0.368426 391 FNBP1L 0.278726302
1.32226 0.3486 768 no value DPY-30-LIKE PROTEIN. [SWISSPROT;Acc:Q9C005] 0.263639526
1.32571 0.502064 93 CBLB SIGNAL TRANSDUCTION PROTEIN CBL-B (SH3-BINDING PROTEIN CBL-B). [SWISSPROT;Acc:Q13191] 0.378713293
1.3266 0.289798 2411 DCP1A TRANSCRIPTION FACTOR SMIF; DECAPPING ENZYME HDCP1A. [RefSeq;Acc:NM_018403] 0.218451681
1.32674 0.349158 780 RBM39 RNA-BINDING REGION CONTAINING PROTEIN 2 (HEPATOCELLULAR CARCINOMA PROTEIN 1) (SPLICING FACTOR HCC1). [SWISSPROT;Acc:Q14498] 0.263169875
1.32794 0.0656147 3184 PYCRL 0.049410892
1.32896 0.351386 754 PRPF3 U4/U6-ASSOCIATED RNA SPLICING FACTOR. [RefSeq;Acc:NM_004698] 0.264406754
1.3291 0.317455 1657 CNNM2 CYCLIN M2; ANCIENT CONSERVED DOMAIN PROTEIN 2. [RefSeq;Acc:NM_017649] 0.238849597
1.32916 0.368948 412 SFRS10 ARGININE/SERINE-RICH SPLICING FACTOR 10 (TRANSFORMER-2-BETA) (HTRA2- BETA) (TRANSFORMER 2 PROTEIN HOMOLOG) (SILICA-INDUCED PROTEIN 41) (RA301). [SWISSPROT;Acc:Q15815] 0.277579825
1.32969 0.31086 1836 LSM1 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM1 (SMALL NUCLEAR RIBONUCLEAR CASM) (CANCER-ASSOCIATED SM-LIKE). [SWISSPROT;Acc:O15116] 0.233783814
1.33096 0.298587 2228 XYLB XYLULOKINASE HOMOLOG; XYLULOKINASE (H. INFLUENZAE) HOMOLOG. [RefSeq;Acc:NM_005108] 0.224339574
1.3313 0.322293 1533 NDUFB10 NADH-UBIQUINONE OXIDOREDUCTASE PDSW SUBUNIT (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-PDSW) (CI-PDSW). [SWISSPROT;Acc:O96000] 0.242088936
1.33263 0.32361 1486 LIN7A LIN-7 HOMOLOG A; VERTEBRATE LIN7 HOMOLOG 1; TAX INTERACTION PROTEIN 33; MAMMALIAN LIN-7 1. [RefSeq;Acc:NM_004664] 0.242835596
1.33367 0.193703 2964 FOXP3 FORKHEAD BOX PROTEIN P3 (ZINC FINGER PROTEIN JM2) (SCURFIN). [SWISSPROT;Acc:Q9BZS1] 0.145240577
1.3344 0.347585 855 STAT6 SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 6 (IL-4 STAT). [SWISSPROT;Acc:P42226] 0.260480366
1.33619 0.157204 3033 UBE2E1 UBIQUITIN-CONJUGATING ENZYME E2 E1 (EC 6.3.2.19) (UBIQUITIN-PROTEIN LIGASE E1) (UBIQUITIN CARRIER PROTEIN E1) (UBCH6). [SWISSPROT;Acc:P51965] 0.117650933
1.33628 0.286606 2552 no value "DNA TOPOISOMERASE II, ALPHA ISOZYME (EC 5.99.1.3). [SWISSPROT;Acc:P11388]" 0.214480498
1.33654 0.335885 1098 CCDC42 0.251309351
1.3369 0.294256 2369 PDSS1 TRANS-PRENYLTRANSFERASE; POLYPRENYL PYROPHOSPHATE SYNTHETASE. [RefSeq;Acc:NM_014317] 0.220103224
1.33704 0.170944 3002 C1orf164 0.12785257
1.33921 0.367035 503 EIF3D EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 7 (EIF-3 ZETA) (EIF3 P66) (EIF3D). [SWISSPROT;Acc:O15371] 0.274068294
1.34026 0.286436 2563 YWHAB 14-3-3 PROTEIN BETA/ALPHA (PROTEIN KINASE C INHIBITOR PROTEIN-1) (KCIP-1) (PROTEIN 1054). [SWISSPROT;Acc:P31946] 0.213716742
1.34189 0.308754 2045 LSM4 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM4 (GLYCINE-RICH PROTEIN) (GRP). [SWISSPROT;Acc:Q9Y4Z0] 0.230088904
1.3435 0.416665 258 EIF3B EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 9 (EIF-3 ETA) (EIF3 P116) (EIF3 P110) (EIF3B). [SWISSPROT;Acc:P55884] 0.310133978
1.34352 0.259669 2830 CLEC3B TETRANECTIN PRECURSOR (TN) (PLASMINOGEN-KRINGLE 4 BINDING PROTEIN). [SWISSPROT;Acc:P05452] 0.193275128
1.3445 0.355858 724 ARPC1A ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 1A (SOP2-LIKE PROTEIN). [SWISSPROT;Acc:Q92747] 0.264676832
1.34662 0.341129 1039 HSP90AB1 HEAT SHOCK PROTEIN HSP 90-BETA (HSP 84) (HSP 90). [SWISSPROT;Acc:P08238] 0.253322392
1.34686 0.425718 229 KIF2A KINESIN-LIKE PROTEIN KIF2 (KINESIN-2) (HK2). [SWISSPROT;Acc:O00139] 0.31608185
1.34852 0.05032 3191 FIBCD1 0.037314982
1.34923 0.311095 2017 SDHB "SUCCINATE DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN, MITOCHONDRIAL PRECURSOR (EC 1.3.5.1) (IP) (IRON-SULFUR SUBUNIT OF COMPLEX II). [SWISSPROT;Acc:P21912]" 0.230572252
1.35049 0.474383 148 FKBP15 0.351267318
1.35164 0.343318 1013 TAF11 TRANSCRIPTION INITIATION FACTOR TFIID 28 KDA SUBUNIT (TAFII-28) (TAFII28) (TFIID SUBUNIT P30-BETA). [SWISSPROT;Acc:Q15544] 0.254001065
1.35261 0.353001 834 FUBP1 FAR UPSTREAM ELEMENT-BINDING PROTEIN; FAR UPSTREAM ELEMENT BINDING PROTEIN; FUSE-BINDING PROTEIN. [RefSeq;Acc:NM_003902] 0.260977665
1.35288 0.321031 1720 MDN1 MIDASIN (MIDAS-CONTAINING PROTEIN). [SWISSPROT;Acc:Q9NU22] 0.237294512
1.35464 0.30758 2166 no value 60S RIBOSOMAL PROTEIN L7. [SWISSPROT;Acc:P18124] 0.227056635
1.35491 0.326192 1588 EIF5A2 EIF-5A2 PROTEIN. [RefSeq;Acc:NM_020390] 0.240748094
1.3576 0.343832 1044 ASCC1 0.253264585
1.35854 0.379312 374 UFD1L UBIQUITIN FUSION DEGRADATION PROTEIN 1 HOMOLOG (UB FUSION PROTEIN 1). [SWISSPROT;Acc:Q92890] 0.279205618
1.36159 0.419259 266 EIF3C EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 8 (EIF3 P110) (EIF3C). [SWISSPROT;Acc:Q99613] 0.307918683
1.36198 0.341608 1116 EIF3M DENDRITIC CELL PROTEIN. [RefSeq;Acc:NM_006360] 0.250817193
1.36407 0.3063 2225 HAO2 "HYDROXYACID OXIDASE 2 (EC 1.1.3.15) (HAOX2) ((S)-2-HYDROXY-ACID OXIDASE, PEROXISOMAL) (LONG CHAIN ALPHA-HYDROXY ACID OXIDASE) (LONG- CHAIN L-2-HYDROXY ACID OXIDASE). [SWISSPROT;Acc:Q9NYQ3]" 0.224548594
1.365 0.365822 648 no value RAN-BINDING PROTEIN 2-LIKE 1 ISOFORM 2; SPERM MEMBRANE PROTEIN BS-63; RAN-BINDING PROTEIN 2-LIKE 1. [RefSeq;Acc:NM_032260] 0.268001465

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/