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 description expected measured Hugo final
Results: HTML CSV LaTeX Showing element 1502 to 1551 of 3206 in total
Rank
description
expected
measured
Hugo
final
1502 "CIRHIN; TESTIS EXPRESSED GENE 292; CIRRHOSIS, AUTOSOMAL RECESSIVE 1A. [RefSeq;Acc:NM_032830]" 2.42296 0.588096 CIRH1A 0.242717998
1503 ZUOTIN RELATED FACTOR-1 (M-PHASE PHOSPHOPROTEIN 11). [SWISSPROT;Acc:Q99543] 0.112006 0.0271819 ZRF1 0.242682535
1504 GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT-LIKE PROTEIN 12.3 (P205) (RECEPTOR OF ACTIVATED PROTEIN KINASE C 1) (RACK1) (RECEPTOR FOR ACTIVATED C KINASE). [SWISSPROT;Acc:P25388] 0.461933 0.112103 no value 0.24268238
1505 PBK1 PROTEIN. [SPTREMBL;Acc:O76021] 2.00168 0.485772 RSL1D1 0.242682147
1506 WD-REPEAT PROTEIN BING4. [SWISSPROT;Acc:O15213] 2.31688 0.562114 WDR46 0.242616795
1507 2.10953 0.511781 NOC4L 0.242604277
1508 PROBABLE RIBOSOME BIOGENESIS PROTEIN NEP1 (C2F PROTEIN). [SWISSPROT;Acc:Q92979] EMG1
1509 EXOCYST COMPLEX COMPONENT SEC6. [SWISSPROT;Acc:O60645] 0.158229 0.0383868 EXOC3 0.24260281
1510 0.474687 0.11516 C19orf50 0.242601967
1511 0.105559 0.0256005 NGDN 0.242523139
1512 APOPTOSIS ANTAGONIZING TRANSCRIPTION FACTOR. [RefSeq;Acc:NM_012138] 1.89991 0.46077 AATF 0.242522014
1513 0.36491 0.0884483 ATPBD4 0.242383875
1514 1.37021 0.332106 WDSOF1 0.242375986
1515 KELCH-LIKE ECH-ASSOCIATED PROTEIN 1 (CYTOSOLIC INHIBITOR OF NRF2). [SWISSPROT;Acc:Q14145] 0.346067 0.0838767 KEAP1 0.242371275
1516 DNA REPLICATION LICENSING FACTOR MCM3 (DNA POLYMERASE ALPHA HOLOENZYME-ASSOCIATED PROTEIN P1) (RLF BETA SUBUNIT) (P102 PROTEIN) (P1-MCM3). [SWISSPROT;Acc:P25205] 0.115356 0.0279589 MCM3 0.242370575
1517 GLIA MATURATION FACTOR GAMMA (GMF-GAMMA). [SWISSPROT;Acc:O60234] 0.278856 0.0675774 GMFG 0.242337981
1518 SUPPRESSOR OF CYTOKINE SIGNALING 1 (SOCS-1) (JAK-BINDING PROTEIN) (JAB) (STAT INDUCED STAT INHIBITOR 1) (SSI-1) (TEC-INTERACTING PROTEIN 3) (TIP-3). [SWISSPROT;Acc:O15524] 0.13962 0.0338352 SOCS1 0.242337774
1519 FK506-BINDING PROTEIN 1A (EC 5.2.1.8) (PEPTIDYL-PROLYL CIS-TRANS ISOMERASE) (PPIASE) (ROTAMASE) (12 KDA FKBP) (FKBP-12) (IMMUNOPHILIN FKBP12). [SWISSPROT;Acc:P20071] FKBP1A
1520 0.665535 0.161284 PAN3 0.242337368
1521 ASC-1 COMPLEX SUBUNIT P100. [RefSeq;Acc:NM_032204] 0.139062 0.0336999 ASCC2 0.242337231
1522 0.417534 0.101184 RBM22 0.242337151
1523 NUCLEOLAR PROTEIN NOP56 (NUCLEOLAR PROTEIN 5A). [SWISSPROT;Acc:O00567] 2.73239 0.66215 NOL5A 0.242333635
1524 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE M1 CHAIN (EC 1.17.4.1) (RIBONUCLEOTIDE REDUCTASE LARGE CHAIN). [SWISSPROT;Acc:P23921] 0.509096 0.123369 RRM1 0.242329541
1525 KINESIN-LIKE PROTEIN KIF3B (MICROTUBULE PLUS END-DIRECTED KINESIN MOTOR 3B) (HH0048). [SWISSPROT;Acc:O15066] 0.43488 0.105382 KIF3B 0.242324319
1526 DOWN-REGULATED IN METASTASIS. [RefSeq;Acc:NM_014503] 4.8561 1.17672 UTP20 0.242317909
1527 "RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 3; RHOGEF PROTEIN; 59.8 KDA PROTEIN; EXCHANGE FACTOR FOUND IN PLATELETS AND LEUKEMIC AND NEURONAL TISSUES, XPLN. [RefSeq;Acc:NM_019555]" 0.0922076 0.0223435 ARHGEF3 0.242317336
1528 NEUROEPITHELIAL CELL TRANSFORMING GENE 1; GUANINE NUCLEOTIDE REGULATORY PROTEIN (ONCOGENE); RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR (GEF) 8. [RefSeq;Acc:NM_005863] 0.105652 0.0256013 NET1 0.24231723
1529 KINESIN-LIKE PROTEIN KIF3C. [SWISSPROT;Acc:O14782] 0.350755 0.0849863 KIF3C 0.242295334
1530 EUKARYOTIC TRANSLATION INITIATION FACTOR 6 (EIF-6) (B4 INTEGRIN INTERACTOR) (CAB) (P27(BBP)) (B(2)GCN HOMOLOG). [SWISSPROT;Acc:P56537] 3.51033 0.850503 EIF6 0.242285768
1531 ATP-DEPENDENT RNA HELICASE ROK1; ATP-DEPENDENT RNA HELICASE. [RefSeq;Acc:NM_007010] 0.315775 0.0764864 DDX52 0.242218035
1532 NIN ONE BINDING PROTEIN; ADENOCARCINOMA ANTIGEN RECOGNIZED BY T LYMPHOCYTES 4. [RefSeq;Acc:NM_014062] 0.332683 0.0805704 NOB1 0.2421837
1533 NADH-UBIQUINONE OXIDOREDUCTASE PDSW SUBUNIT (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-PDSW) (CI-PDSW). [SWISSPROT;Acc:O96000] 1.3313 0.322293 NDUFB10 0.242088936
1534 IRON-RESPONSIVE ELEMENT BINDING PROTEIN 1 (IRE-BP 1) (IRON REGULATORY PROTEIN 1) (IRP1) (FERRITIN REPRESSOR PROTEIN) (ACONITATE HYDRATASE) (EC 4.2.1.3) (CITRATE HYDRO-LYASE) (ACONITASE). [SWISSPROT;Acc:P21399] 0.806892 0.195279 ACO1 0.242013801
1535 UBIQUITIN-CONJUGATING ENZYME E2 N (EC 6.3.2.19) (UBIQUITIN-PROTEIN LIGASE N) (UBIQUITIN CARRIER PROTEIN N) (UBC13) (BENDLESS-LIKE UBIQUITIN CONJUGATING ENZYME). [SWISSPROT;Acc:Q16781] 0.546679 0.132301 UBE2N 0.242008564
1536 "5-FORMYLTETRAHYDROFOLATE CYCLO-LIGASE (EC 6.3.3.2) (5,10-METHENYL- TETRAHYDROFOLATE SYNTHETASE) (METHENYL-THF SYNTHETASE) (MTHFS). [SWISSPROT;Acc:P49914]" 0.285651 0.0691225 MTHFS 0.241982349
1537 "INHIBITOR OF GROWTH FAMILY, MEMBER 1; INHIBITOR OF GROWTH 1. [RefSeq;Acc:NM_005537]" 0.459981 0.111297 ING1 0.241959994
1538 TRANSLATION INITIATION FACTOR EIF-2B DELTA SUBUNIT (EIF-2B GDP-GTP EXCHANGE FACTOR). [SWISSPROT;Acc:Q9UI10] 1.18956 0.287772 EIF2B4 0.241914658
1539 HISTONE H3.3 (H3.A) (H3.B) (H3.3Q). [SWISSPROT;Acc:P06351] 0.906671 0.21933 no value 0.241906932
1540 DJ1099D15.1 (PUTATIVE DNAJ PROTEIN). [SPTREMBL;Acc:Q9H4J9] 0.0887019 0.0214576 0.241906881
1541 "DNA-DIRECTED RNA POLYMERASES I, II, AND III 17.1 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB17) (RPB8) (RPABC3). [SWISSPROT;Acc:P52434]" 1.42971 0.345751 POLR2H 0.241832959
1542 NUCLEAR FACTOR NF-KAPPA-B P100/P49 SUBUNITS (H2TF1) (ONCOGENE LYT-10) (LYT10) [CONTAINS: NUCLEAR FACTOR NF-KAPPA-B P52 SUBUNIT]. [SWISSPROT;Acc:Q00653] 1.71705 0.415216 NFKB2 0.2418194
1543 NF-KAPPAB INHIBITOR BETA (NF-KAPPA-BIB) (I-KAPPA-B-BETA) (IKAPPABBETA) (IKB-BETA) (IKB-B) (THYROID RECEPTOR INTERACTING PROTEIN 9) (TR- INTERACTING PROTEIN 9). [SWISSPROT;Acc:Q15653] 1.71495 0.414708 NFKBIB 0.241819295
1544 NUCLEAR FACTOR NF-KAPPA-B P105 SUBUNIT (DNA-BINDING FACTOR KBF1) (EBP- 1) [CONTAINS: NUCLEAR FACTOR NF-KAPPA-B P50 SUBUNIT]. [SWISSPROT;Acc:P19838] 1.71846 0.415555 NFKB1 0.241818256
1545 B-CELL LYMPHOMA 3-ENCODED PROTEIN (BCL-3 PROTEIN). [SWISSPROT;Acc:P20749] 1.75491 0.424367 BCL3 0.241816959
1546 "INHIBITOR OF GROWTH FAMILY, MEMBER 1-LIKE; INHIBITOR OF GROWTH 1-LIKE. [RefSeq;Acc:NM_001564]" 0.548709 0.132686 ING2 0.241814878
1547 NF-KAPPAB INHIBITOR EPSILON (NF-KAPPA-BIE) (I-KAPPA-B-EPSILON) (IKAPPABEPSILON) (IKB-EPSILON) (IKBE). [SWISSPROT;Acc:O00221] 2.33188 0.56383 NFKBIE 0.24179203
1548 VACUOLAR ATP SYNTHASE SUBUNIT D (EC 3.6.3.14) (V-ATPASE D SUBUNIT) (VACUOLAR PROTON PUMP D SUBUNIT) (V-ATPASE AC39 SUBUNIT) (V-ATPASE 40 KDA ACCESSORY PROTEIN) (P39) (32 KDA ACCESSORY PROTEIN). [SWISSPROT;Acc:P12953] 2.4172 0.584458 ATP6V0D1 0.241791329
1549 ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 4. [SWISSPROT;Acc:P40617] 0.122715 0.0296714 ARL4A 0.241791142
1550 ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 7 (ADP-RIBOSYLATION FACTOR-LIKE PROTEIN LAK). [SWISSPROT;Acc:P56559] 0.150941 0.0364961 no value 0.241790501
1551 0.53787 0.129986 PDRG1 0.241668061

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/