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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Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 908 to 957 of 3206 in total
Rank
description
measured
expected
final
Hugo
908 SEROLOGICALLY DEFINED COLON CANCER ANTIGEN 16. [RefSeq;Acc:NM_006649] 0.0771492 0.298726 0.258260747 UTP14A
909 NEUROTRIMIN PRECURSOR (HNT). [SWISSPROT;Acc:Q9P121] 0.159907 0.619267 0.258219799 no value
910 0.233873 0.906259 0.258064196 CCDC85A
911 LYMPHOID ENHANCER BINDING FACTOR 1 (LEF-1) (T CELL-SPECIFIC TRANSCRIPTION FACTOR 1-ALPHA) (TCF1-ALPHA). [SWISSPROT;Acc:Q9UJU2] 0.427985 1.6585 0.258055472 LEF1
912 0.0349547 0.135465 0.258034917 SLC37A2
913 GLYCEROL-3-PHOSPHATE TRANSPORTER (G-3-P TRANSPORTER) (G-3-P PERMEASE). [SWISSPROT;Acc:P57057] 0.0275088 0.106609 0.2580345 SLC37A1
914 "PROLINE OXIDASE, MITOCHONDRIAL PRECURSOR (EC 1.5.3.-) (PROLINE DEHYDROGENASE). [SWISSPROT;Acc:O43272]" 0.198381 0.768816 0.258034432 PRODH
915 INTERLEUKIN-4 INDUCED PROTEIN 1 PRECURSOR (FIG-1 PROTEIN). [SWISSPROT;Acc:Q96RQ9] 0.19466 0.754632 0.257953546 IL4I1
916 VACUOLAR PROTEIN SORTING 33A (HVPS33A). [SWISSPROT;Acc:Q96AX1] 0.132652 0.514271 0.257941824 VPS33A
917 VACUOLAR PROTEIN SORTING 33B (HVPS33B). [SWISSPROT;Acc:Q9H267] 0.104198 0.40396 0.25794138 VPS33B
918 VACUOLAR PROTEIN SORTING 11 (HVPS11) (PP3476). [SWISSPROT;Acc:Q9H270] 0.167384 0.648924 0.257940837 VPS11
919 RAL GUANINE NUCLEOTIDE EXCHANGE FACTOR RALGPS1A. [RefSeq;Acc:NM_014636] 0.0509651 0.197588 0.257936211 RALGPS1
920 RAL-A EXCHANGE FACTOR RALGPS2. [RefSeq;Acc:NM_152663] 0.040067 0.155337 0.257935971 RALGPS2
921 STIP1 HOMOLOGY AND U-BOX CONTAINING PROTEIN 1; SEROLOGICALLY DEFINED COLON CANCER ANTIGEN 7; CARBOXY TERMINUS OF HSP70P-INTERACTING PROTEIN; HEAT SHOCK PROTEIN A BINDING PROTEIN 2 (C-TERMINAL). [RefSeq;Acc:NM_005861] 0.419455 1.6262 0.257935678 STUB1
922 ALPHA CRYSTALLIN C CHAIN (SMALL STRESS PROTEIN-LIKE PROTEIN HSP22) (E2IG1) (PROTEIN KINASE H11). [SWISSPROT;Acc:Q9UJY1] 0.208436 0.808729 0.257732813 HSPB8
923 HEAT SHOCK 27 KDA PROTEIN (HSP 27) (STRESS-RESPONSIVE PROTEIN 27) (SRP27) (ESTROGEN-REGULATED 24 KDA PROTEIN) (28 KDA HEAT SHOCK PROTEIN). [SWISSPROT;Acc:P04792] 0.28007 1.08675 0.257713366 HSPB1
924 FATTY ACID DESATURASE 1; LINOLEOYL-COA DESATURASE (DELTA-6-DESATURASE)-LIKE 1; DELTA-5 DESATURASE; DELTA-5 FATTY ACID DESATURASE. [RefSeq;Acc:NM_013402] 0.0378274 0.1468 0.257679837 no value
925 FATTY ACID DESATURASE 3; LINOLEOYL-COA DESATURASE (DELTA-6-DESATURASE)-LIKE 3; DELTA-6 FATTY ACID DESATURASE. [RefSeq;Acc:NM_021727] 0.0325155 0.126186 0.25767914 FADS3
926 GERANYLGERANYL TRANSFERASE TYPE I BETA SUBUNIT (EC 2.5.1.-) (TYPE I PROTEIN GERANYL-GERANYLTRANSFERASE BETA SUBUNIT) (GGTASE-I-BETA). [SWISSPROT;Acc:P53609] 0.0378747 0.146984 0.257679067 PGGT1B
927 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 4 (SMAD 4) (MOTHERS AGAINST DPP HOMOLOG 4) (DELETION TARGET IN PANCREATIC CARCINOMA 4) (HSMAD4). [SWISSPROT;Acc:Q13485] 0.303187 1.17661 0.257678415 SMAD4
928 FATTY ACID DESATURASE 2; LINOLEOYL-COA DESATURASE (DELTA-6-DESATURASE)-LIKE 2; DELTA-6 FATTY ACID DESATURASE. [RefSeq;Acc:NM_004265] 0.0336801 0.130706 0.257678301 FADS2
929 PROTEIN TRANSLATION FACTOR SUI1 HOMOLOG (SUI1ISO1). [SWISSPROT;Acc:P41567] 0.546429 2.12125 0.257597643 EIF1
930 DYNEIN LIGHT CHAIN 2. [RefSeq;Acc:NM_080677] 0.266007 1.03319 0.257461841 DYNLL2
931 SHORT COILED-COIL PROTEIN; SHORT COILED COIL PROTEIN. [RefSeq;Acc:NM_032547] 0.0348108 0.135208 0.257461097 SCOC
932 LIMKAIN BETA 2. [RefSeq;Acc:NM_025140] 0.167087 0.649575 0.257225109 CCDC92
933 ADENYLOSUCCINATE LYASE (EC 4.3.2.2) (ADENYLOSUCCINASE) (ASL) (ASASE). [SWISSPROT;Acc:P30566] 0.289435 1.12698 0.256823546 ADSL
934 CYCLIN C. [SWISSPROT;Acc:P24863] 0.0849609 0.330921 0.256740733 CCNC
935 PROTEIN TARA (TRIO-ASSOCIATED REPEAT ON ACTIN) (HRIHFB2122). [SWISSPROT;Acc:Q9H2D6] 0.0598365 0.233092 0.256707652 TRIOBP
936 RHO INTERACTING PROTEIN 3. [RefSeq;Acc:NM_015134] 0.0739754 0.28817 0.256707499 no value
937 IMPORTIN ALPHA-6 SUBUNIT (KARYOPHERIN ALPHA-5 SUBUNIT). [SWISSPROT;Acc:O15131] 1.37404 5.35803 0.256444999 KPNA6
938 CHOLINE O-ACETYLTRANSFERASE (EC 2.3.1.6) (CHOACTASE) (CHOLINE ACETYLASE) (CHAT). [SWISSPROT;Acc:P28329] 0.0510434 0.199072 0.256406727 CHAT
939 YIP1 INTERACTING FACTOR HOMOLOG; YIP1P-INTERACTING FACTOR; PUTATIVE RAB5-INTERACTING PROTEIN; PUTATIVE TRANSMEMBRANE PROTEIN 54TMP. [RefSeq;Acc:NM_020470] 0.121116 0.472359 0.256406674 YIF1A
940 "METHYLMALONATE-SEMIALDEHYDE DEHYDROGENASE [ACYLATING], MITOCHONDRIAL PRECURSOR (EC 1.2.1.27) (MMSDH). [SWISSPROT;Acc:Q02252]" 0.0637409 0.248593 0.256406657 ALDH6A1
941 VOLTAGE-GATED POTASSIUM CHANNEL BETA-3 SUBUNIT (K+ CHANNEL BETA-3 SUBUNIT) (KV-BETA-3). [SWISSPROT;Acc:O43448] 0.0570543 0.222515 0.256406534 KCNAB3
942 0.0943614 0.368015 0.256406396 C1orf121
943 AFLATOXIN B1 ALDEHYDE REDUCTASE 2 (EC 1.-.-.-) (AFB1-AR 2). [SWISSPROT;Acc:O95154] 0.0645005 0.251556 0.256406128 AKR7A3
944 ALPHA/BETA HYDROLASE DOMAIN CONTAINING PROTEIN 3; LUNG ALPHA/BETA HYDROLASE 3. [RefSeq;Acc:NM_138340] 0.0204392 0.0797142 0.25640601 ABHD3
945 AFLATOXIN B1 ALDEHYDE REDUCTASE 1 (EC 1.-.-.-) (AFB1-AR 1) (ALDOKETOREDUCTASE 7). [SWISSPROT;Acc:O43488] 0.0621197 0.242271 0.256405843 AKR7A2
946 VOLTAGE-GATED POTASSIUM CHANNEL BETA-2 SUBUNIT (K+ CHANNEL BETA-2 SUBUNIT) (KV-BETA-2) (HKVBETA2). [SWISSPROT;Acc:Q13303] 0.0586077 0.228574 0.256405803 KCNAB2
947 GOLGI MEMBRANE PROTEIN SB140; SMOOTH MUSCLE CELL ASSOCIATED PROTEIN 5. [RefSeq;Acc:NM_030799] 0.174649 0.681143 0.256405777 YIPF5
948 RAB ACCEPTOR 1 (PRENYLATED); PRENYLATED RAB ACCEPTOR 1. [RefSeq;Acc:NM_006423] 0.13204 0.514965 0.256405775 RABAC1
949 "OLIGORIBONUCLEASE, MITOCHONDRIAL PRECURSOR (EC 3.1.-.-) (SMALL FRAGMENT NUCLEASE) (CGI-114). [SWISSPROT;Acc:Q9Y3B8]" 0.0337699 0.131705 0.256405603 REXO2
950 VOLTAGE-GATED POTASSIUM CHANNEL BETA-1 SUBUNIT (K+ CHANNEL BETA-1 SUBUNIT) (KV-BETA-1). [SWISSPROT;Acc:Q14722] 0.0645342 0.251688 0.25640555 KCNAB1
951 "10 KDA HEAT SHOCK PROTEIN, MITOCHONDRIAL (HSP10) (10 KDA CHAPERONIN) (CPN10). [SWISSPROT;Acc:Q04984]" HSPE1
952 SIMILAR TO PUTATIVE TRANSMEMBRANE PROTEIN; HOMOLOG OF YEAST GOLGI MEMBRANE PROTEIN YIF1P (YIP1P-INTERACTING FACTOR). [RefSeq;Acc:NM_033557] 0.135079 0.526818 0.256405438 YIF1B
953 ALPHA/BETA HYDROLASE DOMAIN CONTAINING PROTEIN 1 ISOFORM 2; LUNG ALPHA/BETA HYDROLASE PROTEIN 1. [RefSeq;Acc:NM_152870] 0.0261125 0.101841 0.256404591 ABHD1
954 IMPORTIN ALPHA-1 SUBUNIT (KARYOPHERIN ALPHA-1 SUBUNIT) (SRP1-BETA) (RAG COHORT PROTEIN 2) (NUCLEOPROTEIN INTERACTOR 1) (NPI-1). [SWISSPROT;Acc:P52294] 1.24311 4.84902 0.256363141 KPNA1
955 VACUOLAR PROTEIN SORTING 16 (HVPS16). [SWISSPROT;Acc:Q9H269] 0.209882 0.818777 0.256335974 PTPRA
956 60S RIBOSOMAL PROTEIN L24 (L30). [SWISSPROT;Acc:P38663] 0.308685 1.20423 0.256333923 RPL24
957 CTP SYNTHASE (EC 6.3.4.2) (UTP--AMMONIA LIGASE) (CTP SYNTHETASE). [SWISSPROT;Acc:P17812] 0.288835 1.12692 0.256304795 CTPS

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/