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 Rank measured Hugo description final
Results: HTML CSV LaTeX Showing element 1202 to 1251 of 3206 in total
expected
Rank
measured
Hugo
description
final
0.367745 512 0.1005 CLK3 PROTEIN KINASE CLK3 (EC 2.7.1.-) (CDC-LIKE KINASE 3). [SWISSPROT;Acc:P49761] 0.273287196
0.367782 2568 0.078494 HDAC5 HISTONE DEACETYLASE 5 (HD5) (ANTIGEN NY-CO-9). [SWISSPROT;Acc:Q9UQL6] 0.213425344
0.368015 942 0.0943614 C1orf121 0.256406396
0.368359 1662 0.0879782 PRUNE2 0.238838199
0.368655 118 0.133134 CAPNS1 "CALCIUM-DEPENDENT PROTEASE, SMALL SUBUNIT (CALPAIN REGULATORY SUBUNIT) (CALCIUM-ACTIVATED NEUTRAL PROTEINASE) (CANP). [SWISSPROT;Acc:P04632]" 0.361134394
0.36903 354 0.103996 TAF7L "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]" 0.281809067
0.369099 168 0.12614 TOE1 "TARGET OF EGR1, MEMBER 1 (NUCLEAR); TARGET OF EGR1, MEMBER 1. [RefSeq;Acc:NM_025077]" 0.341751129
0.369182 1411 0.0900822 RBM10 RNA-BINDING PROTEIN 10 (RNA BINDING MOTIF PROTEIN 10) (DXS8237E). [SWISSPROT;Acc:P98175] 0.244004854
0.370007 2567 0.0789696 ZYG11B 0.213427314
0.370389 891 0.0962556 PRR5 RHO-GTPASE-ACTIVATING PROTEIN 8. [SWISSPROT;Acc:Q9NSG0] 0.259877048
0.371275 2721 0.0767473 NDUFA12 NADH-UBIQUINONE OXIDOREDUCTASE SUBUNIT B17.2 (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-B17.2) (CI-B17.2) (CIB17.2) (13 KDA DIFFERENTIATION-ASSOCIATED PROTEIN). [SWISSPROT;Acc:Q9UI09] 0.206712814
0.371472 2137 0.0846644 TALDO1 TRANSALDOLASE (EC 2.2.1.2). [SWISSPROT;Acc:P37837] 0.227915967
0.371714 3054 0.0392019 GNA11 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(Y), ALPHA SUBUNIT (ALPHA-11). [SWISSPROT;Acc:P29992]" 0.105462533
0.37176 187 0.122271 SH2D3C SH2 DOMAIN CONTAINING 3C; NOVEL SH2-CONTAINING PROTEIN 3; SH2 DOMAIN-CONTAINING 3C; LIKELY ORTHOLOG OF MOUSE CAS/HEF1-ASSOCIATED SIGNAL TRANSDUCER. [RefSeq;Acc:NM_005489] 0.328897676
0.371844 2342 0.0820717 PPP1R2 PROTEIN PHOSPHATASE INHIBITOR 2 (IPP-2). [SWISSPROT;Acc:P41236] 0.220715408
0.372159 702 0.0987306 EPS8L1 EPIDERMAL GROWTH FACTOR RECEPTOR PATHWAY SUBSTRATE 8-LIKE PROTEIN 1 ISOFORM C; EPIDERMAL GROWTH FACTOR RECEPTOR PATHWAY SUBSTRATE 8-RELATED PROTEIN 1; EPS8-RELATED PROTEIN 1. [RefSeq;Acc:NM_139204] 0.265291448
0.372361 975 0.095104 SON SON PROTEIN (SON3) (NEGATIVE REGULATORY ELEMENT-BINDING PROTEIN) (NRE- BINDING PROTEIN) (DBP-5) (BAX ANTAGONIST SELECTED IN SACCHAROMYCES 1) (BASS1) (PROTEIN C21ORF50). [SWISSPROT;Acc:P18583] 0.255408058
0.372425 346 0.1052 DYRK1B DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1B (EC 2.7.1.-) (MIRK PROTEIN KINASE). [SWISSPROT;Acc:Q9Y463] 0.282472981
0.372839 783 0.0979343 WBP2 WW DOMAIN BINDING PROTEIN 2 (WBP-2). [SWISSPROT;Acc:Q969T9] 0.262671823
0.373698 385 0.104222 DYNC1I1 "DYNEIN INTERMEDIATE CHAIN 1, CYTOSOLIC (DH IC-1) (CYTOPLASMIC DYNEIN INTERMEDIATE CHAIN 1). [SWISSPROT;Acc:O14576]" 0.278893652
0.374722 2853 0.0716408 IDH2 "ISOCITRATE DEHYDROGENASE [NADP], MITOCHONDRIAL PRECURSOR (EC 1.1.1.42) (OXALOSUCCINATE DECARBOXYLASE) (IDH) (NADP+-SPECIFIC ICDH) (IDP) (ICD-M). [SWISSPROT;Acc:P48735]" 0.191183864
0.375112 662 0.100197 CHDH CHOLINE DEHYDROGENASE. [RefSeq;Acc:NM_018397] 0.267112222
0.375141 585 0.101295 PPP2R2C "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 55 KDA REGULATORY SUBUNIT B, GAMMA ISOFORM (PP2A, SUBUNIT B, B-GAMMA ISOFORM) (PP2A, SUBUNIT B, B55-GAMMA ISOFORM) (PP2A, SUBUNIT B, PR55-GAMMA ISOFORM) (PP2A, SUBUNIT B, R2-GAMMA ISOFORM) (IMYPNO1). [SWISSP" 0.270018473
0.375337 3055 0.0395834 GNAQ "GUANINE NUCLEOTIDE-BINDING PROTEIN G(Q), ALPHA SUBUNIT. [SWISSPROT;Acc:P50148]" 0.105460959
0.375912 117 0.135756 GCA GRANCALCIN. [SWISSPROT;Acc:P28676] 0.361137713
0.375987 2223 0.0845016 PSAT1 PHOSPHOSERINE AMINOTRANSFERASE (EC 2.6.1.52) (PSAT). [SWISSPROT;Acc:Q9Y617] 0.224746068
0.377297 1017 0.0957789 HRB NUCLEOPORIN-LIKE PROTEIN RIP (HIV-1 REV-BINDING PROTEIN) (REV INTERACTING PROTEIN) (REV/REX ACTIVATION DOMAIN-BINDING PROTEIN). [SWISSPROT;Acc:P52594] 0.253855451
0.377878 272 0.115432 NPC2 EPIDIDYMAL SECRETORY PROTEIN E1 PRECURSOR (NIEMANN-PICK DISEASE TYPE C2 PROTEIN) (EPI-1) (HE1) (EPIDIDYMAL SECRETORY PROTEIN 14.6) (ESP14.6). [SWISSPROT;Acc:Q15668] 0.305474254
0.378775 1477 0.092033 SIP1 SURVIVAL OF MOTOR NEURON PROTEIN-INTERACTING PROTEIN 1 (SMN- INTERACTING PROTEIN 1) (COMPONENT OF GEMS 2) (GEMIN2). [SWISSPROT;Acc:O14893] 0.242975381
1478 DDX20 PROBABLE ATP-DEPENDENT RNA HELICASE DDX20 (DEAD-BOX PROTEIN 20) (DEAD- BOX PROTEIN DP 103) (COMPONENT OF GEMS 3) (GEMIN3). [SWISSPROT;Acc:Q9UHI6]
0.378961 2719 0.0784199 MCTP2 0.206933959
0.379834 802 0.099521 NEGR1 A KINDRED OF IGLON. [RefSeq;Acc:NM_173808] 0.262011826
0.380173 2906 0.0662042 MAN2B1 "LYSOSOMAL ALPHA-MANNOSIDASE PRECURSOR (EC 3.2.1.24) (MANNOSIDASE, ALPHA B) (LYSOSOMAL ACID ALPHA-MANNOSIDASE) (LAMAN) (MANNOSIDASE ALPHA CLASS 2B MEMBER 1). [SWISSPROT;Acc:O00754]" 0.174142298
0.380812 40 0.160294 GRAP2 GRB2-RELATED ADAPTOR PROTEIN 2 (GADS PROTEIN) (GROWTH FACTOR RECEPTOR BINDING PROTEIN) (GRBLG) (GRF40 ADAPTOR PROTEIN) (GRF-40) (GRB-2-LIKE PROTEIN) (GRB2L) (GRBX) (P38) (HEMATOPOIETIC CELL-ASSOCIATED ADAPTOR PROTEIN GRPL) (ADAPTER PROTEIN GRID) (SH3-SH2- 0.420926862
0.380846 116 0.137538 SRI SORCIN (22 KDA PROTEIN) (CP-22) (V19). [SWISSPROT;Acc:P30626] 0.361138098
0.380861 843 0.0992922 LRRC15 LEUCINE-RICH REPEAT-CONTAINING PROTEIN 15 PRECURSOR (HLIB). [SWISSPROT;Acc:Q8TF66] 0.260704562
0.381544 2670 0.0798317 no value TRANSCRIPTION FACTOR MAFG (V-MAF MUSCULOAPONEUROTIC FIBROSARCOMA ONCOGENE HOMOLOG G) (HMAF). [SWISSPROT;Acc:O15525] 0.209233273
0.382047 2944 0.0588972 SF4 SPLICING FACTOR 4 ISOFORM B; RNA-BINDING PROTEIN. [RefSeq;Acc:NM_021164] 0.154162184
0.382068 2547 0.0819968 COX10 "PROTOHEME IX FARNESYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.5.1.-) (HEME O SYNTHASE). [SWISSPROT;Acc:Q12887]" 0.214613106
0.382985 1714 0.0909039 NOLA2 "NUCLEOLAR PROTEIN FAMILY A, MEMBER 2; COMPONENT OF THE H/ACA SNORNP. [RefSeq;Acc:NM_017838]" 0.237356293
0.383122 625 0.102776 CYP4F22 0.268259197
0.383295 1138 0.0959848 TYRL "TYROSINASE-RELATED GENE SEGMENT, EXON 5 (FRAGMENT). [SPTREMBL;Acc:Q15677]" 0.250420172
0.38338 1364 0.0938754 HIST1H2BL HISTONE H2B.C (H2B/C). [SWISSPROT;Acc:Q99880] 0.244862538
0.383993 700 0.101882 EPS8 EPIDERMAL GROWTH FACTOR RECEPTOR KINASE SUBSTRATE EPS8. [SWISSPROT;Acc:Q12929] 0.265322545
0.384447 1634 0.0919591 IMPA2 INOSITOL-1(OR 4)-MONOPHOSPHATASE 2 (EC 3.1.3.25) (IMPASE 2) (IMP 2) (INOSITOL MONOPHOSPHATASE 2) (MYO-INOSITOL MONOPHOSPHATASE A2). [SWISSPROT;Acc:O14732] 0.239198381
0.384928 2080 0.0881768 LDB2 LIM DOMAIN BINDING 2; LIM BINDING DOMAIN 2; LIM DOMAIN-BINDING FACTOR-2. [RefSeq;Acc:NM_001290] 0.229073489
0.384945 1367 0.0942586 no value HISTONE H2B.E (H2B/E). [SWISSPROT;Acc:Q99879] 0.244862513
0.385154 1371 0.0943097 HISTONE H2B. [RefSeq;Acc:NM_175055] 0.244862315
0.385361 472 0.105796 COPS3 COP9 CONSTITUTIVE PHOTOMORPHOGENIC HOMOLOG SUBUNIT 3; COP9 COMPLEX SUBUNIT 3; JAB1-CONTAINING SIGNALOSOME SUBUNIT 3. [RefSeq;Acc:NM_003653] 0.274537382
0.385556 1705 0.0916612 ACTR1B BETA-CENTRACTIN (ACTIN-RELATED PROTEIN 1B) (ARP1B). [SWISSPROT;Acc:P42025] 0.237737709

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/