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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description expected measured Rank Gene final Hugo
Results: HTML CSV LaTeX Showing element 1101 to 1150 of 3206 in total
description
expected
measured
Rank
final
Hugo
ANDROGEN-INDUCED 1; CGI-103 PROTEIN; ANDROGEN INDUCED PROTEIN. [RefSeq;Acc:NM_016108] 0.87768 0.281345 208 0.320555328 AIG1
ANGIOMOTIN LIKE 2; LEMAN COILED-COIL PROTEIN; ANGIOMOTIN-LIKE PROTEIN 2. [RefSeq;Acc:NM_016201] 0.259184 0.064293 1211 0.248059294 AMOTL2
ANGIOMOTIN. [RefSeq;Acc:NM_133265] 0.323509 0.0802494 1214 0.24805925 AMOT
ANKYRIN 3 (ANK-3) (ANKYRIN G). [SWISSPROT;Acc:Q12955] 0.128045 0.0299967 1818 0.234266859 ANK3
ANKYRIN-REPEAT FAMILY A PROTEIN 2 (RFXANK-LIKE 2). [SWISSPROT;Acc:Q9H9E1] 0.573028 0.15014 804 0.262011629 ANKRA2
ANNEXIN A11 (ANNEXIN XI) (CALCYCLIN-ASSOCIATED ANNEXIN 50) (CAP-50) (56 KDA AUTOANTIGEN). [SWISSPROT;Acc:P50995] 0.451047 0.114013 1048 0.252774101 ANXA11
ANNEXIN A7 (ANNEXIN VII) (SYNEXIN). [SWISSPROT;Acc:P20073] 0.590289 0.149169 1052 0.252705031 ANXA7
ANTITHROMBIN-III PRECURSOR (ATIII) (PRO0309). [SWISSPROT;Acc:P01008] 0.230542 0.0555356 1585 0.240891464 SERPINC1
APG3P; PC3-96 PROTEIN. [RefSeq;Acc:NM_022488] 1.59883 0.206188 3000 0.128961803 ATG3
APICAL-LIKE PROTEIN (APXL PROTEIN). [SWISSPROT;Acc:Q13796] 0.30421 0.117195 88 0.385243746 SHROOM2
APOBEC-1 COMPLEMENTATION FACTOR ISOFORM 1; APOBEC-1 STIMULATING PROTEIN; APO-B RNA EDITING PROTEIN. [RefSeq;Acc:NM_014576] 0.180015 0.0555455 261 0.308560398 no value
APOLIPOPROTEIN A-I BINDING PROTEIN; APOA-I BINDING PROTEIN. [RefSeq;Acc:NM_144772] 0.813521 0.180926 2284 0.222398684 APOA1BP
APOLIPOPROTEIN B-100 PRECURSOR (APO B-100) [CONTAINS: APOLIPOPROTEIN B-48 (APO B-48)]. [SWISSPROT;Acc:P04114] 0.125741 0.0307397 1387 0.244468391 APOB
APOPAIN PRECURSOR (EC 3.4.22.-) (CYSTEINE PROTEASE CPP32) (YAMA PROTEIN) (CPP-32) (CASPASE-3) (CASP-3) (SREBP CLEAVAGE ACTIVITY 1) (SCA-1). [SWISSPROT;Acc:P42574] 0.0954818 0.0223509 1829 0.234085449 CASP3
APOPTOSIS ANTAGONIZING TRANSCRIPTION FACTOR. [RefSeq;Acc:NM_012138] 1.89991 0.46077 1512 0.242522014 AATF
APOPTOSIS INHIBITOR 5; FIBROBLAST GROWTH FACTOR 2-INTERACTING FACTOR 2; API5-LIKE 1. [RefSeq;Acc:NM_006595] 0.27327 0.0646874 1755 0.236716068 API5
APOPTOSIS INHIBITOR FKSG2. [SWISSPROT;Acc:Q9HAU6] 0.239562 0.0544712 2148 0.227378299 no value
APOPTOSIS-INDUCING FACTOR (AIF)-HOMOLOGOUS MITOCHONDRION-ASSOCIATED INDUCER OF DEATH; P53-RESPONSIVE GENE 3. [RefSeq;Acc:NM_032797] 1.15907 0.259882 2232 0.224215966 AIFM2
APURINIC/APYRIMIDINIC ENDONUCLEASE 2; APURINIC/APYRIMIDINIC ENDONUCLEASE-LIKE 2; APEX NUCLEASE-LIKE 2. [RefSeq;Acc:NM_014481] 0.305877 0.0730689 1655 0.238883277 APEX2
AQUAPORIN 4 (WCH4) (MERCURIAL-INSENSITIVE WATER CHANNEL) (MIWC). [SWISSPROT;Acc:P55087] 0.311107 0.0599642 2843 0.192744618 AQP4
AQUAPORIN 5. [SWISSPROT;Acc:P55064] 0.313678 0.0604602 2842 0.192746064 AQP5
AQUAPORIN-CD (AQP-CD) (WATER CHANNEL PROTEIN FOR RENAL COLLECTING DUCT) (ADH WATER CHANNEL) (AQUAPORIN 2) (COLLECTING DUCT WATER CHANNEL PROTEIN) (WCH-CD). [SWISSPROT;Acc:P41181] 0.315691 0.0608484 2841 0.192746705 AQP2
AQUAPORIN-CHIP (WATER CHANNEL PROTEIN FOR RED BLOOD CELLS AND KIDNEY PROXIMAL TUBULE) (AQUAPORIN 1) (AQP-1) (URINE WATER CHANNEL). [SWISSPROT;Acc:P29972] 0.415411 0.0800859 2839 0.192787143 AQP1
ARF GTPASE-ACTIVATING PROTEIN GIT1 (G PROTEIN-COUPLED RECEPTOR KINASE- INTERACTOR 1). [SWISSPROT;Acc:Q9Y2X7] 1.28396 0.319576 1182 0.24889872 GIT1
ARF GTPASE-ACTIVATING PROTEIN GIT2 (G PROTEIN-COUPLED RECEPTOR KINASE- INTERACTOR 2). [SWISSPROT;Acc:Q14161] 1.39492 0.345758 1229 0.247869412 GIT2
ARG/ABL-INTERACTING PROTEIN 2 ISOFORM 2; ARG BINDING PROTEIN 2. [RefSeq;Acc:NM_021069] 2.39909 0.864436 121 0.360318287 SORBS2
ARGINASE 1 (EC 3.5.3.1) (LIVER-TYPE ARGINASE). [SWISSPROT;Acc:P05089] 0.945747 0.222245 1790 0.234994137 ARG1
ARGININE-GLUTAMIC ACID DIPEPTIDE (RE) REPEATS; ATROPHIN 1-LIKE; ARGININE GLUTAMIC ACID DIPEPTIDE RE REPEATS. [RefSeq;Acc:NM_012102] 0.63809 0.176985 431 0.277366829 RERE
ARGININE/SERINE-RICH SPLICING FACTOR 10 (TRANSFORMER-2-BETA) (HTRA2- BETA) (TRANSFORMER 2 PROTEIN HOMOLOG) (SILICA-INDUCED PROTEIN 41) (RA301). [SWISSPROT;Acc:Q15815] 1.32916 0.368948 412 0.277579825 SFRS10
ARGININOSUCCINATE LYASE (EC 4.3.2.1) (ARGINOSUCCINASE) (ASAL). [SWISSPROT;Acc:P04424] 1.14373 0.255929 2243 0.223766973 ASL
ARGININOSUCCINATE SYNTHASE (EC 6.3.4.5) (CITRULLINE--ASPARTATE LIGASE). [SWISSPROT;Acc:P00966] 0.685844 0.161564 1778 0.235569605 ASS1
ARGINYL-TRNA SYNTHETASE-LIKE; ARGININE-TRNA LIGASE. [RefSeq;Acc:NM_020320] 0.968873 0.21385 2341 0.220720363 RARS2
ARMET PROTEIN PRECURSOR (ARGININE-RICH PROTEIN). [SWISSPROT;Acc:P55145] 0.403767 0.0869714 2496 0.215399971 ARMET
ARP2/3 COMPLEX 16 KDA SUBUNIT (P16-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 5). [SWISSPROT;Acc:O15511] 1.52156 0.402903 717 0.264795999 ARPC5
ARP2/3 COMPLEX 21 KDA SUBUNIT (P21-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 3). [SWISSPROT;Acc:O15145] 1.48471 0.392968 725 0.264676604 ARPC3
ARP2/3 COMPLEX 34 KDA SUBUNIT (P34-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 2). [SWISSPROT;Acc:O15144] 1.62441 0.427564 778 0.263211874 ARPC2
ARP2/3 COMPLEX 41 KDA SUBUNIT (P41-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 1B). [SWISSPROT;Acc:O15143] 1.20127 0.317947 732 0.264675718 ARPC1B
ARSENICAL PUMP-DRIVING ATPASE (EC 3.6.3.16) (ARSENITE-TRANSLOCATING ATPASE) (ARSENICAL RESISTANCE ATPASE) (ARSENITE-TRANSPORTING ATPASE) (ARSA) (ASNA-I). [SWISSPROT;Acc:O43681] 2.48653 0.539817 2443 0.217096516 no value
ARYL-HYDROCARBON INTERACTING PROTEIN-LIKE 1. [SWISSPROT;Acc:Q9NZN9] 0.178518 0.0410498 2050 0.22994768 AIPL1
ASC-1 COMPLEX SUBUNIT P100. [RefSeq;Acc:NM_032204] 0.139062 0.0336999 1521 0.242337231 ASCC2
ASPARAGINE SYNTHETASE [GLUTAMINE-HYDROLYZING] (EC 6.3.5.4) (GLUTAMINE- DEPENDENT ASPARAGINE SYNTHETASE) (TS11 CELL CYCLE CONTROL PROTEIN). [SWISSPROT;Acc:P08243] 0.137154 0.0326245 1697 0.237867652 ASNS
ASPARTATE BETA-HYDROXYLASE ISOFORM B; JUNCTIN ISOFORM 1; JUNCTATE; ASPARTYL/ASPARAGINYL-BETA-HYDROXYLASE; PEPTIDE-ASPARTATE BETA-DIOXYGENASE; HUMBUG. [RefSeq;Acc:NM_032468] 0.157168 0.06383 78 0.406125929 no value
ASPARTYL-TRNA SYNTHETASE (EC 6.1.1.12) (ASPARTATE--TRNA LIGASE) (ASPRS). [SWISSPROT;Acc:P14868] 0.712692 0.149127 2665 0.209244667 DARS
ASSOCIATED MOLECULE WITH THE SH3 DOMAIN OF STAM (AMSH) LIKE PROTEIN. [RefSeq;Acc:NM_020799] 0.387764 0.0142939 3192 0.03686237 STAMBPL1
ASSOCIATED MOLECULE WITH THE SH3 DOMAIN OF STAM. [RefSeq;Acc:NM_006463] 0.486357 0.0179282 3195 0.036862223 STAMBP
ATAXIN 2 RELATED PROTEIN ISOFORM A; ATAXIN-2 DOMAIN PROTEIN. [RefSeq;Acc:NM_007245] 0.353426 0.070265 2800 0.198811067 ATXN2L
ATAXIN 2-BINDING PROTEIN. [SWISSPROT;Acc:Q9NWB1] 1.96129 0.534301 515 0.272423252 no value
ATAXIN-1 UBIQUITIN-LIKE INTERACTING PROTEIN. [RefSeq;Acc:NM_020131] 1.74675 0.427194 1383 0.244565049 UBQLN4
ATLASTIN; GUANYLATE-BINDING PROTEIN 3. [RefSeq;Acc:NM_015915] 0.81025 0.000178236 3204 0.000219977 no value
ATP SYNTHASE MITOCHONDRIAL F1 COMPLEX ASSEMBLY FACTOR 2. [RefSeq;Acc:NM_145691] 0.356562 0.0993399 394 0.278604843 ATPAF2

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/