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 Rank Gene measured expected final Hugo
Results: HTML CSV LaTeX Showing element 801 to 850 of 3206 in total
description
Rank
measured
expected
final
Hugo
"PYRUVATE KINASE, M1 ISOZYME (EC 2.7.1.40) (PYRUVATE KINASE MUSCLE ISOZYME) (CYTOSOLIC THYROID HORMONE-BINDING PROTEIN) (CTHBP) (THBP1). [SWISSPROT;Acc:P14618]" 2894 0.184777 1.05445 0.175235431 PKM2
"RABAPTIN, RAB GTPASE BINDING EFFECTOR PROTEIN 1; RABAPTIN-5; NEUROCRESCIN. [RefSeq;Acc:NM_004703]" 863 0.0441578 0.169647 0.260292254 RABEP1
"RAC-BETA SERINE/THREONINE PROTEIN KINASE (EC 2.7.1.-) (RAC-PK-BETA) (PROTEIN KINASE AKT-2) (PROTEIN KINASE B, BETA) (PKB BETA). [SWISSPROT;Acc:P31751]" 1437 0.0211896 0.0870115 0.24352643 AKT2
"RAC-GAMMA SERINE/THREONINE PROTEIN KINASE (EC 2.7.1.-) (RAC-PK-GAMMA) (PROTEIN KINASE AKT-3) (PROTEIN KINASE B, GAMMA) (PKB GAMMA) (STK-2). [SWISSPROT;Acc:Q9Y243]" 1440 0.0249436 0.102427 0.243525633 AKT3
"RED CELL ACID PHOSPHATASE 1, ISOZYME F (EC 3.1.3.2) (ACP1) (LOW MOLECULAR WEIGHT PHOSPHOTYROSINE PROTEIN PHOSPHATASE) (EC 3.1.3.48) (ADIPOCYTE ACID PHOSPHATASE, ISOZYME ALPHA). [SWISSPROT;Acc:P24666]" 2846 0.0987604 0.514942 0.191789367 ACP1
"RHESUS BLOOD GROUP, B GLYCOPROTEIN; RH TYPE B GLYCOPROTEIN. [RefSeq;Acc:NM_020407]" 2584 0.0646696 0.303444 0.21311873 RHBG
"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]" 1527 0.0223435 0.0922076 0.242317336 ARHGEF3
"RIBOSOMAL PROTEIN P0-LIKE PROTEIN; 60S ACIDIC RIBOSOMAL PROTEIN PO; RIBOSOMAL PROTEIN, LARGE, P0-LIKE. [RefSeq;Acc:NM_016183]" 1773 0.797221 3.37861 0.235961238 MRTO4
"RIBOSOMAL PROTEIN S6 KINASE, 52KDA, POLYPEPTIDE 1; RIBOSOMAL PROTEIN S6 KINASE, 52KD, POLYPEPTIDE 1. [RefSeq;Acc:NM_012424]" 3168 0.0509886 0.812069 0.062788507 RPS6KC1
"RNA, U TRANSPORTER 1; SNURPORTIN-1. [RefSeq;Acc:NM_005701]" 509 0.0968147 0.353554 0.273832852 SNUPN
"RUNT-RELATED TRANSCRIPTION FACTOR 2 (CORE-BINDING FACTOR, ALPHA 1 SUBUNIT) (CBF-ALPHA 1) (ACUTE MYELOID LEUKEMIA 3 PROTEIN) (ONCOGENE AML-3) (POLYOMAVIRUS ENHANCER BINDING PROTEIN 2 ALPHA A SUBUNIT) (PEBP2-ALPHA A) (PEA2-ALPHA A) (SL3-3 ENHANCER FACTOR 1 " 2130 0.0548378 0.24054 0.227977883 RUNX2
"SELENIDE,WATER DIKINASE 1 (EC 2.7.9.3) (SELENOPHOSPHATE SYNTHETASE 1) (SELENIUM DONOR PROTEIN 1). [SWISSPROT;Acc:P49903]" 102 0.0620748 0.166067 0.37379371 SEPHS1
"SELENIDE,WATER DIKINASE 2 (EC 2.7.9.3) (SELENOPHOSPHATE SYNTHETASE 2) (SELENIUM DONOR PROTEIN 2). [SWISSPROT;Acc:Q99611]" 103 0.0447647 0.119758 0.373792983 SEPHS2
"SERINE HYDROXYMETHYLTRANSFERASE, CYTOSOLIC (EC 2.1.2.1) (SERINE METHYLASE) (GLYCINE HYDROXYMETHYLTRANSFERASE) (SHMT). [SWISSPROT;Acc:P34896]" 1926 0.494954 2.13521 0.231805771 SHMT1
"SERINE HYDROXYMETHYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.2.1) (SERINE METHYLASE) (GLYCINE HYDROXYMETHYLTRANSFERASE) (SHMT). [SWISSPROT;Acc:P34897]" 1903 0.413255 1.77935 0.232250541 SHMT2
"SERINE PROTEASE HTRA2, MITOCHONDRIAL PRECURSOR (EC 3.4.21.-) (HIGH TEMPERATURE REQUIREMENT PROTEIN A2) (HTRA2) (OMI STRESS-REGULATED ENDOPROTEASE) (SERINE PROTEINASE OMI). [SWISSPROT;Acc:O43464]" 2577 0.4666 2.18902 0.213154745 HTRA2
"SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 55 KDA REGULATORY SUBUNIT B, ALPHA ISOFORM (PP2A, SUBUNIT B, B-ALPHA ISOFORM) (PP2A, SUBUNIT B, B55-ALPHA ISOFORM) (PP2A, SUBUNIT B, PR55-ALPHA ISOFORM) (PP2A, SUBUNIT B, R2-ALPHA ISOFORM). [SWISSPROT;Acc:Q0" 582 0.0948257 0.351165 0.270031751 no value
"SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 55 KDA REGULATORY SUBUNIT B, BETA ISOFORM (PP2A, SUBUNIT B, B-BETA ISOFORM) (PP2A, SUBUNIT B, B55- BETA ISOFORM) (PP2A, SUBUNIT B, PR55-BETA ISOFORM) (PP2A, SUBUNIT B, R2-BETA ISOFORM). [SWISSPROT;Acc:Q00005" 584 0.0961987 0.356254 0.270028407 PPP2R2B
"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" 585 0.101295 0.375141 0.270018473 PPP2R2C
"SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 56 KDA REGULATORY SUBUNIT, ALPHA ISOFORM (PP2A, B SUBUNIT, B' ALPHA ISOFORM) (PP2A, B SUBUNIT, B56 ALPHA ISOFORM) (PP2A, B SUBUNIT, PR61 ALPHA ISOFORM) (PP2A, B SUBUNIT, R5 ALPHA ISOFORM). [SWISSPROT;Acc:Q15" 2952 0.057253 0.387696 0.147674982 PPP2R5A
"SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 56 KDA REGULATORY SUBUNIT, EPSILON ISOFORM (PP2A, B SUBUNIT, B' EPSILON ISOFORM) (PP2A, B SUBUNIT, B56 EPSILON ISOFORM) (PP2A, B SUBUNIT, PR61 EPSILON ISOFORM) (PP2A, B SUBUNIT, R5 EPSILON ISOFORM). [SWISSPR" 2953 0.0735334 0.497941 0.147674925 PPP2R5E
"SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 65 KDA REGULATORY SUBUNIT A, ALPHA ISOFORM (PP2A, SUBUNIT A, PR65-ALPHA ISOFORM) (PP2A, SUBUNIT A, R1-ALPHA ISOFORM) (MEDIUM TUMOR ANTIGEN-ASSOCIATED 61 KDA PROTEIN). [SWISSPROT;Acc:P30153]" 565 0.1722 0.635895 0.270799424 PPP2R1A
"SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 65 KDA REGULATORY SUBUNIT A, BETA ISOFORM (PP2A, SUBUNIT A, PR65-BETA ISOFORM) (PP2A, SUBUNIT A, R1-BETA ISOFORM). [SWISSPROT;Acc:P30154]" 573 0.181797 0.671805 0.270609775 PPP2R1B
"SERINE/THREONINE PROTEIN PHOSPHATASE 2A, CATALYTIC SUBUNIT, ALPHA ISOFORM (EC 3.1.3.16) (PP2A-ALPHA) (REPLICATION PROTEIN C) (RP-C). [SWISSPROT;Acc:P05323]" 1827 0.517007 2.20733 0.234222794 PPP2CA
"SERINE/THREONINE PROTEIN PHOSPHATASE 2B CATALYTIC SUBUNIT, ALPHA ISOFORM (EC 3.1.3.16) (CALMODULIN-DEPENDENT CALCINEURIN A SUBUNIT, ALPHA ISOFORM) (CAM-PRP CATALYTIC SUBUNIT). [SWISSPROT;Acc:Q08209]" 620 0.283215 1.05458 0.268557151 PPP3CA
"SERINE/THREONINE PROTEIN PHOSPHATASE 2B CATALYTIC SUBUNIT, BETA ISOFORM (EC 3.1.3.16) (CALMODULIN-DEPENDENT CALCINEURIN A SUBUNIT, BETA ISOFORM) (CAM-PRP CATALYTIC SUBUNIT). [SWISSPROT;Acc:P16299]" 618 0.232385 0.865296 0.268561278 PPP3CB
"SERINE/THREONINE PROTEIN PHOSPHATASE 2B CATALYTIC SUBUNIT, GAMMA ISOFORM (EC 3.1.3.16) (CALMODULIN-DEPENDENT CALCINEURIN A SUBUNIT, GAMMA ISOFORM) (CALCINEURIN, TESTIS-SPECIFIC CATALYTIC SUBUNIT) (CAM-PRP CATALYTIC SUBUNIT). [SWISSPROT;Acc:P48454]" 617 0.221484 0.824699 0.26856344 PPP3CC
"SERYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRSMT). [SWISSPROT;Acc:Q9NP81]" 1847 0.215775 0.924279 0.233452237 SARS2
"SH2 DOMAIN BINDING PROTEIN 1; TPR-CONTAINING, SH2-BINDING PHOSPHOPROTEIN. [RefSeq;Acc:NM_014633]" 1165 0.144652 0.579965 0.249415051 no value
"SIMILAR TO RIBOSOMAL PROTEIN, LARGE, P0. [SPTREMBL;Acc:Q96FQ9]" 1251 0.100674 0.406955 0.247383617
"SIN3 ASSOCIATED POLYPEPTIDE P30; SIN3-ASSOCIATED POLYPEPTIDE, 30KD. [RefSeq;Acc:NM_003864]" 2904 0.0253172 0.145382 0.174142604 SAP30
"SIRTUIN 7; SIR2-RELATED PROTEIN TYPE 7; SIRTUIN TYPE 7; SIRTUIN (SILENT MATING TYPE INFORMATION REGULATION 2, S.CEREVISIAE, HOMOLOG) 7; SILENT MATING TYPE INFORMATION REGULATION 2, S.CEREVISIAE, HOMOLOG 7; SIRTUIN SILENT MATING TYPE INFORMATION REGULATION" 773 0.0367538 0.139602 0.263275598 no value
"SMALL OPTIC LOBES HOMOLOG; SMALL OPTIC LOBES, DROSOPHILA, HOMOLOG OF. [RefSeq;Acc:NM_005632]" 1079 0.177598 0.704023 0.252261645 SOLH
"SOLUTE CARRIER FAMILY 13, MEMBER 1 (RENAL SODIUM/SULFATE COTRANSPORTER) (NA(+)/SULFATE COTRANSPORTER) (HNASI-1). [SWISSPROT;Acc:Q9BZW2]" 2659 0.0481673 0.229436 0.209937848 SLC13A1
"SOLUTE CARRIER FAMILY 13, MEMBER 2 (RENAL SODIUM/DICARBOXYLATE COTRANSPORTER) (NA(+)/DICARBOXYLATE COTRANSPORTER 1) (NADC-1). [SWISSPROT;Acc:Q13183]" 2660 0.0401827 0.191403 0.209937671 SLC13A2
"SOLUTE CARRIER FAMILY 13, MEMBER 3 (SODIUM-DEPENDENT HIGH-AFFINITY DICARBOXYLATE TRANSPORTER 2) (NA(+)/DICARBOXYLATE COTRANSPORTER 3) (NADC-3) (HNADC3). [SWISSPROT;Acc:Q8WWT9]" 2657 0.0395353 0.188319 0.209937924 SLC13A3
"SOLUTE CARRIER FAMILY 13, MEMBER 4 (NA+/SULFATE COTRANSPORTER SUT-1). [SWISSPROT;Acc:Q9UKG4]" 2658 0.0480531 0.228892 0.209937875 SLC13A4
"SOLUTE CARRIER FAMILY 2, FACILITATED GLUCOSE TRANSPORTER, MEMBER 6 (GLUCOSE TRANSPORTER TYPE 6) (GLUCOSE TRANSPORTER TYPE 9). [SWISSPROT;Acc:Q9UGQ3]" 1244 0.0527752 0.213145 0.247602336 SLC2A6
"SOLUTE CARRIER FAMILY 2, FACILITATED GLUCOSE TRANSPORTER, MEMBER 8 (GLUCOSE TRANSPORTER TYPE 8) (GLUCOSE TRANSPORTER TYPE X1). [SWISSPROT;Acc:Q9NY64]" 1245 0.069385 0.280228 0.247601953 SLC2A8
"SOLUTE CARRIER FAMILY 20 (PHOSPHATE TRANSPORTER), MEMBER 1; GLVR-1; PIT-1; GIBBON APE LEUKEMIA VIRUS RECEPTOR 1. [RefSeq;Acc:NM_005415]" 2362 0.0465225 0.211181 0.220296807 SLC20A1
"SOLUTE CARRIER FAMILY 20 (PHOSPHATE TRANSPORTER), MEMBER 2; GLVR-2; PIT-2; GIBBON APE LEUKEMIA VIRUS RECEPTOR 2; MURINE LEUKEMIA VIRUS, AMPHOTROPIC; RECEPTOR. [RefSeq;Acc:NM_006749]" 2363 0.0378408 0.171772 0.220296672 SLC20A2
"SOLUTE CARRIER FAMILY 23, MEMBER 1 (SODIUM-DEPENDENT VITAMIN C TRANSPORTER 1) (HSVCT1) (NA(+)/L-ASCORBIC ACID TRANSPORTER 1) (YOLK SAC PERMEASE-LIKE MOLECULE 3). [SWISSPROT;Acc:Q9UHI7]" 478 0.0444669 0.162108 0.274304168 SLC23A1
"SOLUTE CARRIER FAMILY 23, MEMBER 2 (SODIUM-DEPENDENT VITAMIN C TRANSPORTER 2) (HSVCT2) (NA(+)/L-ASCORBIC ACID TRANSPORTER 2) (YOLK SAC PERMEASE-LIKE MOLECULE 2) (NUCLEOBASE TRANSPORTER-LIKE 1 PROTEIN). [SWISSPROT;Acc:Q9UGH3]" 482 0.0377969 0.137792 0.274304023 SLC23A2
"SOLUTE CARRIER FAMILY 27 (FATTY ACID TRANSPORTER), MEMBER 4; FATTY ACID TRANSPORT PROTEIN 4. [RefSeq;Acc:NM_005094]" 2717 0.416194 2.00736 0.207334011 SLC27A4
"SOLUTE CARRIER FAMILY 27 (FATTY ACID TRANSPORTER), MEMBER 5; VERY LONG-CHAIN ACYL-COA SYNTHETASE HOMOLOG 2; VERY LONG-CHAIN ACYL-COA SYNTHETASE-RELATED PROTEIN; LIKELY ORTHOLOG OF MOUSE SOLUTE CARRIER FAMILY 27 (FATTY ACID TRANSPORTER), MEMBER 5. [" 2714 0.44721 2.15689 0.207340198 SLC27A5
"SOLUTE CARRIER FAMILY 35, MEMBER B1; UDP-GALACTOSE TRANSPORTER RELATED. [RefSeq;Acc:NM_005827]" 1923 0.0974156 0.419969 0.231959026 SLC35B1
"SOLUTE CARRIER FAMILY 4 (ANION EXCHANGER), MEMBER 1, ADAPTOR PROTEIN; KIDNEY ANION EXCHANGER ADAPTOR PROTEIN; KANADAPTIN; LUNG CANCER ONCOGENE 3. [RefSeq;Acc:NM_018158]" 2876 0.0374428 0.198705 0.188434111 SLC4A1AP
"SOLUTE CARRIER FAMILY 5 (IODIDE TRANSPORTER), MEMBER 8; APICAL IODIDE TRANSPORTER. [RefSeq;Acc:NM_145913]" 2572 0.257307 1.20606 0.213345107 SLC5A8
"SPECTRIN BETA CHAIN, BRAIN 1 (SPECTRIN, NON-ERYTHROID BETA CHAIN 1) (BETA-II SPECTRIN) (FODRIN BETA CHAIN). [SWISSPROT;Acc:Q01082]" 595 0.0426374 0.158312 0.26932513 SPTBN1
"SPECTRIN BETA CHAIN, BRAIN 2 (SPECTRIN, NON-ERYTHROID BETA CHAIN 2) (BETA-III SPECTRIN). [SWISSPROT;Acc:O15020]" 592 0.0341846 0.126926 0.269327009 SPTBN2

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/