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 [...,...].
description Rank Gene measured expected final Hugo
Results: HTML CSV LaTeX Showing element 2508 to 2557 of 3206 in total
description
Rank
measured
expected
final
Hugo
PROTOCADHERIN FAT 2 PRECURSOR (HFAT2) (MULTIPLE EPIDERMAL GROWTH FACTOR-LIKE DOMAINS 1). [SWISSPROT;Acc:Q9NYQ8] 822 0.0300014 0.114826 0.261277063 FAT2
PRP18 PRE-MRNA PROCESSING FACTOR 18 HOMOLOG. [RefSeq;Acc:NM_003675] 1888 0.184055 0.790803 0.232744438 PRPF18
PTB DOMAIN ADAPTOR PROTEIN CED-6; ENGULFMENT ADAPTER PROTEIN. [RefSeq;Acc:NM_016315] 378 0.0573826 0.205572 0.279136264 GULP1
PURINE NUCLEOSIDE PHOSPHORYLASE (EC 2.4.2.1) (INOSINE PHOSPHORYLASE) (PNP). [SWISSPROT;Acc:P00491] 829 0.253043 0.969143 0.261099755 no value
PUROMYCIN-SENSITIVE AMINOPEPTIDASE (EC 3.4.11.-) (PSA). [SWISSPROT;Acc:P55786] 2270 0.0267797 0.120229 0.222739106 NPEPPS
PUTATATIVE 28 KDA PROTEIN. [RefSeq;Acc:NM_020143] 1010 0.222495 0.87407 0.254550551 PNO1
PUTATIVE ACYL-COA THIOESTER HYDROLASE CGI-16 (EC 3.1.2.-). [SWISSPROT;Acc:Q9Y305] 2973 0.231971 1.65329 0.140308718 ACOT9
PUTATIVE ADENOSYLHOMOCYSTEINASE 2 (EC 3.3.1.1) (S-ADENOSYL-L- HOMOCYSTEINE HYDROLASE) (ADOHCYASE). [SWISSPROT;Acc:O43865] 54 0.25896 0.629835 0.411155303 AHCYL1
PUTATIVE ADENOSYLHOMOCYSTEINASE 3 (EC 3.3.1.1) (S-ADENOSYL-L- HOMOCYSTEINE HYDROLASE) (ADOHCYASE). [SWISSPROT;Acc:Q96HN2] 61 0.312681 0.760495 0.411154577 no value
PUTATIVE ANKYRIN-REPEAT CONTAINING PROTEIN. [RefSeq;Acc:NM_025185] 827 0.0298281 0.114163 0.261276421
PUTATIVE BREAST ADENOCARCINOMA MARKER (32KD). [RefSeq;Acc:NM_014453] 3198 0.0100954 0.273869 0.036862149 CHMP2A
PUTATIVE DIMETHYLANILINE MONOOXYGENASE [N-OXIDE FORMING] 6 (EC 1.14.13.8) (FLAVIN-CONTAINING MONOOXYGENASE 6) (FMO 6) (DIMETHYLANILINE OXIDASE 6). [SWISSPROT;Acc:O60774] 1884 0.0627928 0.269788 0.232748677 FMO6P
PUTATIVE EUKARYOTIC TRANSLATION INITIATION FACTOR 1A (EIF-1A) (EIF- 4C). [SWISSPROT;Acc:O75642] 2016 1.27676 5.53686 0.230592791 no value
PUTATIVE EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT (EIF-3) (FRAGMENT). [SWISSPROT;Acc:O75153] 1597 0.275535 1.14705 0.240211848 KIAA0664
PUTATIVE GLIALBLASTOMA CELL DIFFERENTIATION-RELATED; PUTATIVE GLIALBLASTOMA CELL DIFFERENTIATION-RELATED PROTEIN. [RefSeq;Acc:NM_016172] 3177 0.0184372 0.333333 0.055311655 UBAC1
PUTATIVE GTP-BINDING PROTEIN PTD004 (PRO2455). [SWISSPROT;Acc:Q9NTK5] 1149 0.154662 0.618161 0.250196955 OLA1
PUTATIVE INORGANIC POLYPHOSPHATE/ATP-NAD KINASE (EC 2.7.1.23) (POLY(P)/ATP NAD KINASE). [SWISSPROT;Acc:O95544] 1691 0.195442 0.821038 0.238042575 NADK
PUTATIVE N6-DNA-METHYLTRANSFERASE (EC 2.1.1.-) (PROTEIN PRED28) (M.HSAHEMK2P). [SWISSPROT;Acc:Q9Y5N5] 2412 0.357172 1.63578 0.218349656 N6AMT1
PUTATIVE NUCLEOSIDE DIPHOSPHATE KINASE (EC 2.7.4.6) (NDK) (NDP KINASE). [SWISSPROT;Acc:O60361] 2011 0.480816 2.08449 0.230663616 NME2P1
PUTATIVE PHOSPHOGLYCERATE MUTASE 3 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13). [SWISSPROT;Acc:Q8N0Y7] 1097 0.030826 0.122661 0.251310522 PGAM4
PUTATIVE PRE-MRNA SPLICING FACTOR RNA HELICASE (ATP-DEPENDENT RNA HELICASE #3) (DEAH-BOX PROTEIN 16). [SWISSPROT;Acc:O60231] 878 0.039713 0.15268 0.260106104 no value
PUTATIVE PRE-MRNA SPLICING FACTOR RNA HELICASE (DEAH BOX PROTEIN 15) (ATP-DEPENDENT RNA HELICASE #46). [SWISSPROT;Acc:O43143] 408 0.603245 2.16897 0.278125101 DHX15
PUTATIVE RIBOSOMAL RNA METHYLTRANSFERASE 1 (EC 2.1.1.-) (RRNA (URIDINE-2'-O-)-METHYLTRANSFERASE) (JM23 PROTEIN). [SWISSPROT;Acc:Q9UET6] 591 0.12174 0.452001 0.269335687 FTSJ1
PUTATIVE RNA-BINDING PROTEIN 15 (RNA BINDING MOTIF PROTEIN 15) (ONE-TWENTY TWO PROTEIN). [SWISSPROT;Acc:Q96T37] 2929 0.0148857 0.0939662 0.158415473 RBM15
PUTATIVE RNA-BINDING PROTEIN 7 (RNA BINDING MOTIF PROTEIN 7). [SWISSPROT;Acc:Q9Y580] 748 0.0771388 0.291643 0.264497348 RBM7
PUTATIVE SIALOGLYCOPROTEASE TYPE 2. [RefSeq;Acc:NM_022353] 1783 0.365106 1.55176 0.235285096 OSGEPL1
PWWP DOMAIN CONTAINING 1; HDGF (HEPATOMA-DERIVED GROWTH FACTOR) LIKE. [RefSeq;Acc:NM_138574] 2871 0.0294363 0.155797 0.188940095 HDGFL1
PXR2B PROTEIN. [RefSeq;Acc:NM_016559] 248 0.253658 0.812851 0.312059652 PEX5L
PYRIDOXINE 5'-PHOSPHATE OXIDASE. [RefSeq;Acc:NM_018129] 1131 0.0418316 0.166987 0.250508123 PNPO
PYRROLINE 5-CARBOXYLATE REDUCTASE ISOFORM. [RefSeq;Acc:NM_013328] 3157 0.131587 2.02325 0.06503744 PYCR2
PYRROLINE-5-CARBOXYLATE REDUCTASE (EC 1.5.1.2) (P5CR) (P5C REDUCTASE). [SWISSPROT;Acc:P32322] 3132 0.137845 2.1027 0.06555619 PYCR1
QUAKING ISOFORM 6. [SPTREMBL;Acc:Q9P0X9] 545 0.59995 2.2133 0.271065829 QKI
R3H DOMAIN PROTEIN 1. [SWISSPROT;Acc:Q15032] 495 0.309779 1.12934 0.274300919 R3HDM1
RAB ACCEPTOR 1 (PRENYLATED); PRENYLATED RAB ACCEPTOR 1. [RefSeq;Acc:NM_006423] 948 0.13204 0.514965 0.256405775 RABAC1
RAB COUPLING PROTEIN; RAB-INTERACTING RECYCLING PROTEIN; RAB EFFECTOR PROTEIN; RAB11-FAMILY INTERACTING PROTEIN 1. [RefSeq;Acc:NM_025151] 763 0.0360283 0.136657 0.263640355 RAB11FIP1
RAB3A INTERACTING PROTEIN (RABIN3)-LIKE 1. [RefSeq;Acc:NM_013401] 1346 0.197255 0.804471 0.245198397 RAB3IL1
RAB3A INTERACTING PROTEIN ISOFORM ALPHA 1; RABIN3; SSX2 INTERACTING PROTEIN. [RefSeq;Acc:NM_022456] 1344 0.165502 0.674746 0.245280446 RAB3IP
RAC GTPASE ACTIVATING PROTEIN 1; GTPASE ACTIVATING PROTEIN. [RefSeq;Acc:NM_013277] 1301 0.268542 1.09266 0.245769041 RACGAP1
RAC-ALPHA SERINE/THREONINE KINASE (EC 2.7.1.-) (RAC-PK-ALPHA) (PROTEIN KINASE B) (PKB) (C-AKT). [SWISSPROT;Acc:P31749] 1438 0.0218319 0.089649 0.24352642 AKT1
RAD1 HOMOLOG ISOFORM 1; EXONUCLEASE HOMOLOG RAD1; CELL CYCLE CHECKPOINT PROTEIN RAD1 A/B; RAD1-LIKE PROTEIN; CELL CYCLE CHECKPOINT PROTEIN HRAD1; DNA REPAIR EXONUCLEASE (REC1); DNA REPAIR PROTEIN RAD1; RAD1-LIKE DNA DAMAGE CHECKPOINT PROTEIN. [RefS 1308 0.874478 3.55876 0.245725477 RAD1
RAD17 HOMOLOG ISOFORM 1; RAD17-LIKE PROTEIN; CELL CYCLE CHECKPOINT PROTEIN (RAD17); RF-C ACTIVATOR 1 HOMOLOG. [RefSeq;Acc:NM_002873] 1041 0.0746521 0.294737 0.253283775 RAD17
RAD50 HOMOLOG ISOFORM 1. [RefSeq;Acc:NM_005732] 2924 0.168223 1.00248 0.167806839 RAD50
RAD50-INTERACTING PROTEIN 1. [RefSeq;Acc:NM_021930] 2 1.28125 1.1674 1.097524413 RINT1
RAD54-LIKE PROTEIN; RAD54 HOMOLOG. [RefSeq;Acc:NM_003579] 1735 0.180241 0.760447 0.237019805 RAD54L
RAD9 HOMOLOG; CELL CYCLE CHECKPOINT CONTROL PROTEIN; RAD9 HOMOLOG (S. POMBE). [RefSeq;Acc:NM_004584] 1304 0.0763771 0.310798 0.245745146 RAD9A
RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE (EC 2.7.1.-) (RAF-1) (C-RAF). [SWISSPROT;Acc:P04049] 2955 0.219758 1.48848 0.147639202 RAF1
RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR (RALGEF) (RALGDS). [SWISSPROT;Acc:Q12967] 2967 0.122631 0.850955 0.144109853 RALGDS
RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR-LIKE 1 (RALGDS-LIKE 1). [SWISSPROT;Acc:Q9NZL6] 2968 0.106453 0.742944 0.143285362 RGL1
RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR-LIKE 2 (RALGDS-LIKE FACTOR) (RAS-ASSOCIATED PROTEIN RAB2L). [SWISSPROT;Acc:O15211] 2960 0.0746316 0.510598 0.146165085 no value
RAL GUANINE NUCLEOTIDE EXCHANGE FACTOR RALGPS1A. [RefSeq;Acc:NM_014636] 919 0.0509651 0.197588 0.257936211 RALGPS1

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/